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

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

doi:10.1186/2041-1480-1-8

Kiyoko F. Aoki‐Kinoshita , Martin Senger

Open Access

https://doi.org/10.1186/2041-1480-1-8

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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.

Highlights

Web services are software systems designed to be manipulated remotely over a network, often through web-based application programming interfaces (APIs)
Minimal information required for client authentication would include: 1) authorization levels of a user according to UNIX-like permissions, 2) standardized interchange protocols and formats, 3) authentication based on X509 digital certificates, a technology commonly used for secure website connections, 4) certificates managed through a Public Key Infrastructure (PKI), which deals with the secure creation, validation and revocation of certificates, 5) availability of all relevant web services in the case of running a workflow, 6) profiling of offer deployment based on user rights or roles
Standardization efforts for exchange formats and service ontologies reached a certain level of agreement in the areas of biological interactions, phyloinformatics, glycoinformatics, and text-mining

Summary

Introduction

Web services are software systems designed to be manipulated remotely over a network, often through web-based application programming interfaces (APIs). Standardization and interoperability of web services were discussed by experts invited from four different domains: 1) web service providers, 2) Open Bio* developers, 3) workflow client developers, and 4) BioMoby project developers.

Results

Conclusion