Adding text mining workflows as web services to the BioCatalogue

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Georgios Kontonasios, Ioannis Korkontzelos, Bala Krishna Kolluru, Sophia Ananiadou

Published: 01 Dec 2011, Last Modified: 08 Feb 2026SWAT4LS 2011 EveryoneRevisionsBibTeXCC BY-SA 4.0
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.