The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.
Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.
Katayama
Toshiaki
T
Database Center for Life Science, Research Organization of Information and Systems, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan. ktym@hgc.jp.
Arakawa
Kazuharu
K
Nakao
Mitsuteru
M
Ono
Keiichiro
K
Aoki-Kinoshita
Kiyoko F
KF
Yamamoto
Yasunori
Y
Yamaguchi
Atsuko
A
Kawashima
Shuichi
S
Chun
Hong-Woo
HW
Aerts
Jan
J
Aranda
Bruno
B
Barboza
Lord Hendrix
LH
Bonnal
Raoul Jp
RJ
Bruskiewich
Richard
R
Bryne
Jan C
JC
Fernández
José M
JM
Funahashi
Akira
A
Gordon
Paul Mk
PM
Goto
Naohisa
N
Groscurth
Andreas
A
Gutteridge
Alex
A
Holland
Richard
R
Kano
Yoshinobu
Y
Kawas
Edward A
EA
Kerhornou
Arnaud
A
Kibukawa
Eri
E
Kinjo
Akira R
AR
Kuhn
Michael
M
Lapp
Hilmar
H
Lehvaslaiho
Heikki
H
Nakamura
Hiroyuki
H
Nakamura
Yasukazu
Y
Nishizawa
Tatsuya
T
Nobata
Chikashi
C
Noguchi
Tamotsu
T
Oinn
Thomas M
TM
Okamoto
Shinobu
S
Owen
Stuart
S
Pafilis
Evangelos
E
Pocock
Matthew
M
Prins
Pjotr
P
Ranzinger
René
R
Reisinger
Florian
F
Salwinski
Lukasz
L
Schreiber
Mark
M
Senger
Martin
M
Shigemoto
Yasumasa
Y
Standley
Daron M
DM
Sugawara
Hideaki
H
Tashiro
Toshiyuki
T
Trelles
Oswaldo
O
Vos
Rutger A
RA
Wilkinson
Mark D
MD
York
William
W
Zmasek
Christian M
CM
Asai
Kiyoshi
K
Takagi
Toshihisa
T