Journal of Biomedical Semantics (Aug 2010)

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*

  • Katayama Toshiaki,
  • Arakawa Kazuharu,
  • Nakao Mitsuteru,
  • Ono Keiichiro,
  • Aoki-Kinoshita Kiyoko F,
  • Yamamoto Yasunori,
  • Yamaguchi Atsuko,
  • Kawashima Shuichi,
  • Chun Hong-Woo,
  • Aerts Jan,
  • Aranda Bruno,
  • Barboza Lord,
  • Bonnal Raoul JP,
  • Bruskiewich Richard,
  • Bryne Jan C,
  • Fernández José M,
  • Funahashi Akira,
  • Gordon Paul MK,
  • Goto Naohisa,
  • Groscurth Andreas,
  • Gutteridge Alex,
  • Holland Richard,
  • Kano Yoshinobu,
  • Kawas Edward A,
  • Kerhornou Arnaud,
  • Kibukawa Eri,
  • Kinjo Akira R,
  • Kuhn Michael,
  • Lapp Hilmar,
  • Lehvaslaiho Heikki,
  • Nakamura Hiroyuki,
  • Nakamura Yasukazu,
  • Nishizawa Tatsuya,
  • Nobata Chikashi,
  • Noguchi Tamotsu,
  • Oinn Thomas M,
  • Okamoto Shinobu,
  • Owen Stuart,
  • Pafilis Evangelos,
  • Pocock Matthew,
  • Prins Pjotr,
  • Ranzinger René,
  • Reisinger Florian,
  • Salwinski Lukasz,
  • Schreiber Mark,
  • Senger Martin,
  • Shigemoto Yasumasa,
  • Standley Daron M,
  • Sugawara Hideaki,
  • Tashiro Toshiyuki,
  • Trelles Oswaldo,
  • Vos Rutger A,
  • Wilkinson Mark D,
  • York William,
  • Zmasek Christian M,
  • Asai Kiyoshi,
  • Takagi Toshihisa

DOI
https://doi.org/10.1186/2041-1480-1-8
Journal volume & issue
Vol. 1, no. 1
p. 8

Abstract

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Abstract 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.