Software used:
Taverna : Workflow environment of myGrid.

The BioMoby project was initiated to provide greater interoperability between biological data. It aims to provide a platform through which existing and new biological data hosts can:

• Exchange common data representation formats to assist in data integration.
• Provide both manual and automated methods for discovering related data set and services.
• Establish a mechanism for machine-discernable meaning or context for data and services.

BioMoby now offers more than 800 data retrieval and analysis services used by several clients. So far none of these clients have been capable of enabling interoperability between BioMoby services and non-BioMoby services, or of assembling or decomposing BioMoby data types to enhance service discovery.

With BioMoby extension to Taverna, users can now:

• obtain useful information regarding the data types or services.
• Initiate workflow using any BioMoby Object of their choice.
• Compose and decompose BioMoby Object to comply with a wider range of Service interfaces.
• Parse data out of BioMoby's XML message structure such that it can be used as input to non-BioMoby services; enabling interoperability between BioMoby services and non-BioMoby services.
• Access the MOBY Central Web service registry query system to achieve guidance during workflow construction.
• Configure services parameters with guidance and sanity-checking of user-input.
• Construct workflows that automatically make correct decisions on how to package data as it passes between the various services.

The majority of functionality exposed by the MOBY Central API is now available via the Taverna graphical interface. Taverna has become the most fully-featured client for BioMoby web services.

Figure 1 - A BioMoby workflow with Taverna

Paper recently published in BMC Bioinformatics November 2006:

BioMoby extensions to the Taverna workflow management and enactment software Edward A Kawas, Martin Senger and Mark D Wilkinson ,BMC Bioinformatics November 2006, 7:523, doi:10.1186/1471-2105-7-523

Background: As biology becomes an increasingly computational science, it is critical that we develop software tools that support not only bioinformaticians, but also bench biologists in their exploration of the vast and complex data-sets that continue to build from international genomic, proteomic, and systems-biology projects. The BioMoby interoperability system was created with the goal of facilitating the movement of data from one Web-based resource to another to fulfill the requirements of non-expert bioinformaticians. In parallel with the development of BioMoby, the European myGrid project was designing Taverna, a bioinformatics workflow design and enactment tool. Here we describe the marriage of these two projects in the form of a Taverna plug-in that provides access to many of BioMoby's features through the Taverna interface.

Results: The exposed BioMoby functionality aids in the design of "sensible" BioMoby workflows, aids in pipelining BioMoby and non-BioMoby-based resources, and ensures that end-users need only a minimal understanding of both BioMoby, and the Taverna interface itself. Users are guided through the construction of syntactically and semantically correct workflows through plug-in calls to the Moby Central registry. Moby Central provides a menu of only those BioMoby services capable of operating on the data-type(s) that exist at any given position in the workflow. Moreover, the plug-in automatically and correctly connects a selected service into the workflow such that users are not required to understand the nature of the inputs or outputs for any service, leaving them to focus on the biological meaning of the workflow they are constructing, rather than the technical details of how the services will interoperate.

Read the article: http://www.biomedcentral.com/1471-2105/7/523/abstract