BioMOBY Successfully Integrates Distributed Heterogeneous Bioinformatics Web Services. The PlaNet Exemplar Case

Abstract

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.

The Arabidopsis genome: A foundation for plant research

“…net/). This method has been successfully implemented by the PlaNet database Consortium (Wilkinson et al 2005), who provide a comprehensive array of Arabidopsis genome-related data resources through BioMOBY services (http://mips.gsf.de/ projects/plants/PlaNetPortal/index_html).…”

Munich Information Center for Protein Sequences Plant Genome Resources. A Framework for Integrative and Comparative Analyses

“…Recently, Web services have been suggested as a solution to the problem of data and analysis resource interoperability and data integration for biology and bioinformatics (Schoof et al, 2004;Wilkinson et al, 2005). We have decided to support BioMOBY, an emerging standard that builds on Web services and extends these with ontologies that describe data structure, semantics, and service types (Wilkinson and Links, 2002;Wilkinson et al, 2005).…”

“…However, genome-scale bioinformatics analyses are limited by the effort required for data integration (Wilkinson et al, 2005). Regarding plants only, there is already a plethora of data resources worldwide: Arabidopsis data is available from several genome databases, including The Arabidopsis Information Resource (TAIR; http://www.arabidopsis.org), The Institute for Genomic Research (TIGR; http://www.…”

CressExpress: A Tool For Large-Scale Mining of Expression Data from Arabidopsis

“…For more advanced users, the ''web services'' link provides an example of a short R script showing how to import the data into the R statistical programming environment and compute Pearson's correlation coefficient between query genes from the glucosinolates biosynthesis pathway. We also provide several BioMoby services for programmers to incorporate CressExpress functionality into their applications (Wilkinson et al, 2005). We do not describe these here but instead refer readers to the CressExpress ''Web Services'' section, which documents the BioMoby services and their uses.…”