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