BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.
The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed.
Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. ktym@dbcls.jp.
Toshiaki
T
Katayama
Mark D
MD
Wilkinson
Kiyoko F
KF
Aoki-Kinoshita
Shuichi
S
Kawashima
Yasunori
Y
Yamamoto
Atsuko
A
Yamaguchi
Shinobu
S
Okamoto
Shin
S
Kawano
Jin-Dong
JD
Kim
Yue
Y
Wang
Hongyan
H
Wu
Yoshinobu
Y
Kano
Hiromasa
H
Ono
Hidemasa
H
Bono
Simon
S
Kocbek
Jan
J
Aerts
Yukie
Y
Akune
Erick
E
Antezana
Kazuharu
K
Arakawa
Bruno
B
Aranda
Joachim
J
Baran
Jerven
J
Bolleman
Raoul Jp
RJ
Bonnal
Pier Luigi
PL
Buttigieg
Matthew P
MP
Campbell
Yi-An
YA
Chen
Hirokazu
H
Chiba
Peter Ja
PJ
Cock
K Bretonnel
KB
Cohen
Alexandru
A
Constantin
Geraint
G
Duck
Michel
M
Dumontier
Takatomo
T
Fujisawa
Toyofumi
T
Fujiwara
Naohisa
N
Goto
Robert
R
Hoehndorf
Yoshinobu
Y
Igarashi
Hidetoshi
H
Itaya
Maori
M
Ito
Wataru
W
Iwasaki
Matúš
M
Kalaš
Takeo
T
Katoda
Taehong
T
Kim
Anna
A
Kokubu
Yusuke
Y
Komiyama
Masaaki
M
Kotera
Camille
C
Laibe
Hilmar
H
Lapp
Thomas
T
Lütteke
M Scott
MS
Marshall
Takaaki
T
Mori
Hiroshi
H
Mori
Mizuki
M
Morita
Katsuhiko
K
Murakami
Mitsuteru
M
Nakao
Hisashi
H
Narimatsu
Hiroyo
H
Nishide
Yosuke
Y
Nishimura
Johan
J
Nystrom-Persson
Soichi
S
Ogishima
Yasunobu
Y
Okamura
Shujiro
S
Okuda
Kazuki
K
Oshita
Nicki H
NH
Packer
Pjotr
P
Prins
Rene
R
Ranzinger
Philippe
P
Rocca-Serra
Susanna
S
Sansone
Hiromichi
H
Sawaki
Sung-Ho
SH
Shin
Andrea
A
Splendiani
Francesco
F
Strozzi
Shu
S
Tadaka
Philip
P
Toukach
Ikuo
I
Uchiyama
Masahito
M
Umezaki
Rutger
R
Vos
Patricia L
PL
Whetzel
Issaku
I
Yamada
Chisato
C
Yamasaki
Riu
R
Yamashita
William S
WS
York
Christian M
CM
Zmasek
Shoko
S
Kawamoto
Toshihisa
T
Takagi