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Deploying and sharing U-Compare workflows as web services
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 matchin...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3658995/ https://www.ncbi.nlm.nih.gov/pubmed/23419017 http://dx.doi.org/10.1186/2041-1480-4-7 |
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author | Kontonatsios, Georgios Korkontzelos, Ioannis Kolluru, BalaKrishna Thompson, Paul Ananiadou, Sophia |
author_facet | Kontonatsios, Georgios Korkontzelos, Ioannis Kolluru, BalaKrishna Thompson, Paul Ananiadou, Sophia |
author_sort | Kontonatsios, Georgios |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3658995 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-36589952013-05-21 Deploying and sharing U-Compare workflows as web services Kontonatsios, Georgios Korkontzelos, Ioannis Kolluru, BalaKrishna Thompson, Paul Ananiadou, Sophia J Biomed Semantics Software 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. BioMed Central 2013-02-18 /pmc/articles/PMC3658995/ /pubmed/23419017 http://dx.doi.org/10.1186/2041-1480-4-7 Text en Copyright © 2013 Kontonatsios et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Kontonatsios, Georgios Korkontzelos, Ioannis Kolluru, BalaKrishna Thompson, Paul Ananiadou, Sophia Deploying and sharing U-Compare workflows as web services |
title | Deploying and sharing U-Compare workflows as web services |
title_full | Deploying and sharing U-Compare workflows as web services |
title_fullStr | Deploying and sharing U-Compare workflows as web services |
title_full_unstemmed | Deploying and sharing U-Compare workflows as web services |
title_short | Deploying and sharing U-Compare workflows as web services |
title_sort | deploying and sharing u-compare workflows as web services |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3658995/ https://www.ncbi.nlm.nih.gov/pubmed/23419017 http://dx.doi.org/10.1186/2041-1480-4-7 |
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