NCBO-Galaxy: bridging the BioPortal web services and the Galaxy platform

BioPortal (Noy et al. (2009)) is a web-based application for searching, sharing, visualizing, and analyzing bio-ontologies. It has become one of the major, centralised bio-ontologies repositories. BioPortal not only hosts a considerable number of important biomedical ontologies (currently almost 300 ontologies covering various life science domains) but also provides access to its contents via RESTful web services, which are a flexible means for programmatically exploiting the stored ontologies. Consequently, its usage should be promoted in bioinformatics environments for facilitating the usage of bio-ontologies. The lack of integration of bio-ontologies and semantic tools with traditional bioinformatics suites is a major reason for the limited usage of bio-ontologies by bioinformaticians. Galaxy (Goecks et al. (2010)) is a web-based platform offering a one-stop-shop of common bioinformatics tools enabling biological data analyses. The so-called Galaxy tools are executed within an environment that keeps an execution history as well as the output of each executed tool, which can be easily shared and reproduced. Even though Galaxy offers a wide range of tools, and recently, some efforts have provided a few tools for ontology manipulation: ONTOtoolkit (Antezana et al. (2010)), OPPL-Galaxy (Aranguren et al. (2012)), and Blast2GO (Conesa et al. (2005)). Each of them offers a complementary functionality, but none of them provides a mechanism to exploit directly a repository of bio-ontologies, such as BioPortal, without having to upload them prior their exploitation. Therefore, providing Galaxy users with direct access to the BioPortal ontologies seems an interesting option. In this work, we describe the development of a set of Galaxy tools, called NCBO-Galaxy, which provide BioPortal functionalities via its set of RESTful web services (Whetzel et al. (2011)). Such a coupling enables the development of advanced analysis workflows, which eventually could improve data curation and management processes.