Abstract
BackgroundU-Compare is a text mining platform that allows the construction, evaluation and comparison of text mining workflows. U-Compare contains a large library of components that are tuned to the biomedical domain. Users can rapidly develop biomedical text mining workflows by mixing and matching U-Compare’s components. Workflows developed using U-Compare can be exported and sent to other users who, in turn, can import and re-use them. However, the resulting workflows are standalone applications, i.e., software tools that run and are accessible only via a local machine, and that can only be run with the U-Compare platform.ResultsWe address the above issues by extending U-Compare to convert standalone workflows into web services automatically, via a two-click process. The resulting web services can be registered on a central server and made publicly available. Alternatively, users can make web services available on their own servers, after installing the web application framework, which is part of the extension to U-Compare. We have performed a user-oriented evaluation of the proposed extension, by asking users who have tested the enhanced functionality of U-Compare to complete questionnaires that assess its functionality, reliability, usability, efficiency and maintainability. The results obtained reveal that the new functionality is well received by users.ConclusionsThe web services produced by U-Compare are built on top of open standards, i.e., REST and SOAP protocols, and therefore, they are decoupled from the underlying platform. Exported workflows can be integrated with any application that supports these open standards. We demonstrate how the newly extended U-Compare enhances the cross-platform interoperability of workflows, by seamlessly importing a number of text mining workflow web services exported from U-Compare into Taverna, i.e., a generic scientific workflow construction platform.
Highlights
U-Compare is a text mining platform that allows the construction, evaluation and comparison of text mining workflows
U-Compare components and workflows are still platform dependent, i.e., the resulting text mining tools can only be used via U-Compare. We address this problem by making U-Compare workflows available as web services that are built on open standards, i.e., REST and SOAP protocols
In this paper, we have presented an extension of UCompare for transforming text mining workflows into HTTP GET/POST web services
Summary
U-Compare is a text mining platform that allows the construction, evaluation and comparison of text mining workflows. Users can rapidly develop biomedical text mining workflows by mixing and matching U-Compare’s components. The vast majority of text mining systems adopt modular approaches, which combine a number of components, each of which solves a particular subtask, to facilitate robust, scalable text analysis. These components do not normally address a complete text mining task. Text mining workflows provide users with the ability to “mix and match” a variety of components within a workflow. Certain combinations of components may result in a suboptimal workflow that affects the overall performance of a text mining system [1]. It is critical that developers are able to evaluate and compare different workflows [2], in order to discover potential problems and to determine the best performing workflow
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