Adapting the Galaxy Bioinformatics Tool (ISMB DAM SIG 2009)

…to Support Semantic Web Service Composition

Eileen Kramer, University of Georgia

They are working with Galaxy to extend it. Galaxy is available for workflows and uses Yahoo pipes. It’s an open-source project, and is relatively easy to use. Some limitations exist, for instance although it can be used via any browser, all tools must be installed on a server. They’re trying to add improvements such as web services for access to the tools. They’re working mainly on web service composition, and the addition of semantic web services via WSDL-S and SAWSDL. Essentially, they want to be able to invoke web services from within Galaxy. There was then a number of movies to demo how these services work.

Galaxy has a number of different data types, and provides some tools for converting between them. They want to perform data mediation, and use XML data types for the web services. Their data mediation uses a top-down approach: lifting mapping converts to the common ontology, and the lowering mapping sends from the common ontology to the other format.

They want to combine the Galaxy workflow and the web service composition. They plan to extend Galaxy workflow to support web services. One issue – should BPEL be used versus other process definition languages? Another issue is process mediation, and provide suggestions when a user is composing a workflow and have a semi-automatic approach.

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Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!


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