Abstract
BackgroundIn recent years Galaxy has become a popular workflow management system in bioinformatics, due to its ease of installation, use and extension. The availability of Semantic Web-oriented tools in Galaxy, however, is limited. This is also the case for Semantic Web Services such as those provided by the SADI project, i.e. services that consume and produce RDF. Here we present SADI-Galaxy, a tool generator that deploys selected SADI Services as typical Galaxy tools.ResultsSADI-Galaxy is a Galaxy tool generator: through SADI-Galaxy, any SADI-compliant service becomes a Galaxy tool that can participate in other out-standing features of Galaxy such as data storage, history, workflow creation, and publication. Galaxy can also be used to execute and combine SADI services as it does with other Galaxy tools. Finally, we have semi-automated the packing and unpacking of data into RDF such that other Galaxy tools can easily be combined with SADI services, plugging the rich SADI Semantic Web Service environment into the popular Galaxy ecosystem.ConclusionsSADI-Galaxy bridges the gap between Galaxy, an easy to use but “static” workflow system with a wide user-base, and SADI, a sophisticated, semantic, discovery-based framework for Web Services, thus benefiting both user communities.
Highlights
In recent years Galaxy has become a popular workflow management system in bioinformatics, due to its ease of installation, use and extension
There is a growing global movement towards representation of bioinformatics data and knowledge using contemporary syntaxes and semantic languages approved by the World Wide Web Consortium (W3C) [1], like Resource Description Framework (RDF) [2] and Web Ontology Language (OWL) [3]
Semantic Automated Discovery and Integration (SADI)-Galaxy is inspired by the Galaxy Web Services Extensions (GWSE) tool [25,26], which is able to dynamically load SAWSDL/WSDL web services as Galaxy tools
Summary
In recent years Galaxy has become a popular workflow management system in bioinformatics, due to its ease of installation, use and extension. Major bioinformatics resources making their data available using these formats include UniProt [4], EBI [5], and soon, the DNA Databank of Japan [6] Beyond these core providers, there are large integrated warehouses of bioinformatics data in RDF format including, most significantly, Bio2RDF [7], which integrates critical bioinformatics resources such as dbSNP [8], OMIM [9], and KEGG [10], and NCBI eutils [11], which wraps NCBI databases as resolvable RDF resources. The Semantic Automated Discovery and Integration (SADI) project has established design-patterns for bioinformatics resources that wish to natively consume and produce RDF data [12], and there are SADI plug-ins to several popular data workflow and exploration environments, including Taverna [13] and the IO Informatics Sentient Knowledge Explorer [14]. We describe SADI-Galaxy - a set of tools that retrieve and “wrap” SADI Semantic Web Services in a manner that allows them to be included in Galaxy workflows
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