Year: 2013
Type: article
Abstract: BACKGROUND: U-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. RESULTS: We 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. CONCLUSIONS: The 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.
Source: Journal of Biomedical Semantics
Authors: Georgios Kontonatsios, Ioannis Korkontzelos, BalaKrishna Kolluru, Paul Thompson, Sophia Ananiadou
Institution: University of Manchester
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $1,590
Funders: European Commission, Joint Information Systems Committee, Universidade de Lisboa, Universitat Politècnica de Catalunya, Università ta' Malta, Engineering and Physical Sciences Research Council, Biotechnology and Biological Sciences Research Council, Directorate-General for Information Society and Media
OpenAlex ID: W2108345035