The document summarizes BioHackathon 2014 which is organized by NBDC/DBCLS to standardize and utilize human genome information using semantic web technologies. It discusses the mission of NBDC/DBCLS, an overview of past BioHackathon events, examples of linked open data projects including TogoGenome, the use of ontologies, and collaborations with other organizations toward developing common standards for genomics data sharing. The hackathon was held in Sendai, Japan at the Tohoku Medical Megabank Organization which was established after the 2011 earthquake and tsunami to rebuild the community medical system using a biobank combining medical and genome information.

1. NBDC / DBCLS presents
BioHackathon 2014
Standardization and utilization of human genome information
with Semantic Web technologies
Toshiaki Katayama <ktym@dbcls.jp>
http://jp.linkedin.com/in/toshiakikatayama
Database Center for Life Science (DBCLS),
Research Organization of Information and Systems (ROIS), Japan
2014/11/9 @ Tohoku Medical Megabank, Sendai, Japan

2. Hackathon
Excursion...
Symposium

3. Mission of NBDC/DBCLS
• Biomedical domain
• So many databases, so many publications
• Integration of life science databases
• To accelerate data driven science
• Standardization and interoperability
• Semantic Web and Linked Open Data
• Software development
• :
• Right technology + collaborative community
• BioHackathon = Bio + Hack + Marathon = effective innovation

4. http://2014.biohackathon.org
BioHackathon 2014 - the 7th NBDC/DBCLS BioHackathon
• BioHackathon 2008 in Tokyo
• Towards integrated Web service in life science with Open Bio* libraries
• http://hackathon.dbcls.jp
• BioHackathon 2009 in Okinawa
• Integration of Web services in bioinformatics applications
• http://hackathon2.dbcls.jp
• BioHackathon 2010 in Tokyo
• Integration and interpretation of biological knowledge with the Semantic Web technologies
• http://hackathon3.dbcls.jp
• BioHackathon 2011 in Kyoto
• Creation and utilization of Linked Data in life sciences
• http://2011.biohackathon.org
• BioHackathon 2012 in Toyama
• Biomecial applications based on the Semantic Web technologies
• http://2012.biohackathon.org
• BioHackathon 2013 in Tokyo
• Semantic interoperability and standardization of bioinformatics data and Web services
• http://2013.biohackathon.org

5. BioHackathon publications
BioHackathon
thematic series

6. Linked Open Data
• Use URIs as names for things
• Use HTTP URIs
• so that people can look up those names
• When someone looks up a URI
• provide useful information
• using the standards (RDF*, SPARQL)
• Include links to other URIs
• so that they can discover more things

7. http://togogenome.org
TogoGenome: RDF-based genome DB }
• Genome annotation / Protein annotation / Biomedical ontologies / URIs
Regulatory region Protein coding gene rRNA gene
↑ ↑ ↑ ↑
rdfs:subClassOf obo:SO_0000147 .
Accumulate annotations in RDF
Genome
↑ ↑ ↑ ↑
<exon>
<gene> rdfs:subClassOf obo:SO_0000704 ;
faldo:location [ ... ] ;
rdfs:label "geneA" ;
rdfs:seeAlso <UniProt> .
← Sequence ontology types
← FALDO locations
← Label of annotations
← Link to external resources

8. Annotation w/ in-house developed ontologies
Accumulate annotations in RDF
+
In-house developed ontologies
•MEO (environment)
•MPO (phenotype)
•GMO (growth medium)
•MCCV (culture collection)
•PDO (infectious disease)
↓
Stored in triple store
↓
SPARQL query
↓
TogoGenome / TogoStanza
Genome sequences
NCBI: BioProject/RefSeq -- existing reference seqs
DDBJ: Annotation pipeline/GTPS -- newly sequenced
Annotations
UniProt: Protein functions and links
Formats: GFF3, GTF, GVF, DAS, BED, ..
Tools: Cufflinks, BLAST, InterProt, ...
Ontologies
NCBO: BioPortal, OBO (GO, SO, ...)
DBCLS: FALDO, MEO, MPO, GMO, MCCV, PDO ...
DDBJ: INSDC, Taxonomy, ...
Titech: PDO, ...
GOLD: Environmental metadata
Samples and metadata
INSDC, NCBI: SRA, GEO
DBCLS: RefEx, Kusarinoko
Bulk data: Literatures, Images, ...

9. http://togogenome.org
TogoGenome faceted search & modular reports

10. Regulatory region Protein coding gene rRNA gene
↑ ↑ ↑ ↑
rdfs:subClassOf obo:SO_0000147 .
<gene> rdf:type insdc:Gene ;
so:so_part_of <chromosome> .
<mRNA> rdf:type insdc:Messenger_RNA ;
sio:is-transcribed-from <gene> ;
sio:has-ordered-part <p1>, <p2>, ... .
<p1> sio:has-value "1"^^xsd:integer ;
sio:refers-to <exon1> .
<p2> sio:has-value "2"^^xsd:integer ;
sio:refers-to <exon2> .
<exon1> rdf:type insdc:Exon ;
faldo:location <region1> .
<region1> rdf:type faldo:Region ;
faldo:begin <position1> ;
faldo:end <position2> .
← Sequence ontology types
<position1> rdf:type faldo:ExactPosition, faldo:ForwardStrandPosition ;
faldo:position 12345 ;
faldo:reference <chromosome> .
Genome
↑ ↑ ↑ ↑
<exon>
<gene> rdfs:subClassOf obo:SO_0000704 ;
faldo:location [ ... ] ;
rdfs:label "geneA" ;
rdfs:seeAlso <UniProt> .
← FALDO locations
← Label of annotations
← Link to external resources
INSDC/RefSeq/Ensembl RDF:

11. RDF summit May 17-20, 2014
Standardization of RDF models for genomics
INSDC
Standardization of INSDC nucleotide annotations in RDF
Ontology for locations of annotations
Common URIs to be shared
Common RDF model for genomes
Transcriptomes and regulations
Personal/Japanese genomes

12. http://genomicsandhealth.org/
Global Alliance for Genomics and Health
The greatest need was a common framework of international standards
designed to enable and oversee how genomic and clinical data are
shared in an effective, responsible, and interpretable manner.
to develop this common framework, enabling learning from data
while protecting participant autonomy and privacy.
Over 180 organizations world wide (2013-14)
+ Google (since 2014/2/28)
To enable secure sharing of genomic and clinical data

13. 18,487
March 11, 2011

14. http://www9.nhk.or.jp/311shogen/map/

15. Tohoku Medical Megabank Organization
• As one of the reconstruction plans, Tohoku Medical Megabank
Organization was founded for rebuilding the community
medical system by developing a biobank that combines medical
and genome information for supporting health and welfare in
the Tohoku area.

16. Questions?
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