Plant Physiology 138:5-17 (2005)
© 2005 American Society of Plant Biologists
BIOINFORMATICS-PLANT DATABASES
BioMOBY Successfully Integrates Distributed Heterogeneous Bioinformatics Web Services. The PlaNet Exemplar Case1
Mark Wilkinson*,
Heiko Schoof,
Rebecca Ernst and
Dirk Haase
James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St. Paul's Hospital, Department of Medical Genetics, University of British Columbia, Vancouver, Canada (M.W.); Technische Universität München, Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, D–85350 Freising-Weihenstephan, Germany (H.S.); and Institute for Bioinformatics, Gesellschaft für Strahlenforschung National Research Center for Environment and Health, D–85764 Neuherberg, Germany (H.S., R.E., D.H.)
The burden of noninteroperability between on-line genomic resources is increasingly the rate-limiting step in large-scale genomic analysis. BioMOBY is a biological Web Service interoperability initiative that began as a retreat of representatives from the model organism database community in September, 2001. Its long-term goal is to provide a simple, extensible platform through which the myriad of on-line biological databases and analytical tools can offer their information and analytical services in a fully automated and interoperable way. Of the two branches of the larger BioMOBY project, the Web Services branch (MOBY-S) has now been deployed over several dozen data sources worldwide, revealing some significant observations about the nature of the integrative biology problem; in particular, that Web Service interoperability in the domain of bioinformatics is, unexpectedly, largely a syntactic rather than a semantic problem. That is to say, interoperability between bioinformatics Web Services can be largely achieved simply by specifying the data structures being passed between the services (syntax) even without rich specification of what those data structures mean (semantics). Thus, one barrier of the integrative problem has been overcome with a surprisingly simple solution. Here, we present a nontechnical overview of the critical components that give rise to the interoperable behaviors seen in MOBY-S and discuss an exemplar case, the PlaNet consortium, where MOBY-S has been deployed to integrate the on-line plant genome databases and analytical services provided by a European consortium of databases and data service providers.
1 This work was supported by Genome Canada/Genome Prairie, A Bioinformatics Platform for Genome Canada (Dr. Christoph Sensen, Lead Principal Investigator). PlaNet is funded by EU Framework V (grant no. QLRI–CT–2001–00006).
www.plantphysiol.org/cgi/doi/10.1104/pp.104.059170.
* Corresponding author; e-mail mwilkinson{at}mrl.ubc.ca; fax 1–604 –06 –274.
Received December 31, 2004;
returned for revision March 3, 2005;
accepted March 3, 2005.
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