BioHackathon 2015in Nagasaki
Department of Human Genetics,
ABDI, Nagasaki University
MISHIMA, Hiroyuki
CC BY 4.0
1.Brief history of Nagasaki
and Nagasaki University
2.My TO-DO LIST for BH15
1641 – 1859: Dejima – the sole place of direct
trading between Japan and outside world
The Medical School (1857-)
J. L. C. Pompe van Meerdervoot from the Netherlands
A. F. Bauduin from the Nerherlands
B. Ryojyun Matsumoto
Nagasaki Medical College
(about 1900)
College Hospital
(about 1920)
August 9th, 1945
11:02am
1967- Atomic Bomb Disease Institute, Nagasaki University
• Radiation risk control unit
• Cellular function analysis unit
• Genomic function analysis unit
• Dept. of Human Genetics
• Atomic bomb disease and Hibakusha medicine unit
• Center for promotion of collaborative research
Human Genetics ::=
Science of
heredity and
variation
in humans
Dr. Toshihisa Takagi
Director-General,
National Bioscience Database Center
The goal of life
sciences is building
databases!
“Database Biology”
Human Genetics ::=
“Database Biology”
“Database Medicine”
Gene Hunting:
Finding causal genes of
rare and
undiagnosed
diseases
NGS - the break-through
1. Massive Parallel Sequencing
technology (biologists)
2. Nagasaki (IATA)
Combination of NGS
+ public databases
has achieved
a triumph in
gene hunting
Is “NGS +
huge sample sets +
huge databases”
a silver bullet
for gene hunting?
Answer: NO
for rare and undiagnosed diseases
1.Heterogeneity – same
phenotype, different causal
genes
2.Only one patient in the world
3.Can be a non typical case of
known rare disease
Knowledge network –
like a brain of a
remarkable researcher
who knows everything
in a field
Togo picture gallery by DBCLS is licensed under a Creative Commons Attribution 2.1 Japan license (c)
Biohackers’ answer:
The Semantic Web
Technology
American Journal of Human Genetics, 2015
Dr. Tudor Groza (1:15pm -)
Initiative on Rare and
Undiagnosed Diseases
(IRUD)
Dr. Kenjiro Kosaki (1:00pm -)
Mishima’s TO-LIST
• Develop Docker “data containers”
for my favorite RDFs and the
Virtuoso engine (BioVirtuoso)
• RDFize “HPO Annotation”
• Play with SPARQL and the
Knowledge Network
• Japanese Translation of HPO
• Liftover several databases from
hg19 to hg38