Adding text mining workflows as web services to the BioCatalogue

Authors:
Georgios Kontonasios;Ioannis Korkontzelos;BalaKrishna Kolluru;Sophia Ananiadou
Affiliations:
University of Manchester;University of Manchester;University of Manchester;University of Manchester
Venue:
Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences
Year:
2011

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Abstract

In this paper, we address the issue of automatically adding U-Compare workflows to BioCatalogue by exploring the compatibility of UIMA to a REST-like web service. We aim to make workflows consisting of state-of-the-art text mining components available to the bioinformatics community without the need for any expertise in programming or software library dependencies. We present a framework for developing UIMA-compliant, REST-like, text mining services which can either supplement the existing components or be used as bespoke, stand-alone workflows. The framework embodies U-Compare's component library and refactors Apache UIMA SimpleServer to provide a post-processing component of the analysis results, a human-readable access mechanism, and documentation templates. As an application, we implemented a number of new services, which are registered with the BioCatalogue.