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A Web Tool for Generating High Quality Machine-readable Biological Pathways
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Published on: February 8, 2017

Deploying and sharing U-Compare workflows as web services.

Georgios Kontonatsios1, Ioannis Korkontzelos, Balakrishna Kolluru

  • 1National Centre for Text Mining & School of Computer Science, The University of Manchester, Manchester, M1 7DN, UK. georgios.kontonatsios@cs.man.ac.uk.

Journal of Biomedical Semantics
|February 20, 2013
PubMed
Summary
This summary is machine-generated.

U-Compare now converts text mining workflows into web services, enhancing interoperability and accessibility. This extension allows seamless integration with other applications, improving biomedical text mining research and collaboration.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Text Mining

Background:

  • U-Compare is a platform for constructing, evaluating, and comparing text mining workflows, particularly for the biomedical domain.
  • Workflows created in U-Compare are typically standalone applications, limiting their accessibility and reusability outside the U-Compare environment.
  • Existing U-Compare workflows require the U-Compare platform to run and are restricted to local machine execution.

Purpose of the Study:

  • To extend U-Compare by enabling the automatic conversion of standalone text mining workflows into web services.
  • To enhance the accessibility and interoperability of U-Compare workflows beyond the U-Compare platform.
  • To facilitate the integration of U-Compare workflows with other scientific workflow systems and applications.

Main Methods:

  • Developed an extension for U-Compare to automatically convert workflows into web services through a simple, two-click process.
  • Implemented functionality for registering web services on a central server or deploying them on private servers.
  • Conducted a user-oriented evaluation using questionnaires to assess the functionality, reliability, usability, efficiency, and maintainability of the enhanced U-Compare.

Main Results:

  • The extension successfully converts U-Compare workflows into web services.
  • User feedback indicates positive reception of the new web service functionality.
  • The developed web services are built on open standards (REST, SOAP), ensuring platform independence.

Conclusions:

  • The extended U-Compare significantly enhances cross-platform interoperability of text mining workflows.
  • Web services generated by U-Compare can be integrated with any application supporting REST and SOAP protocols.
  • Demonstrated successful integration of U-Compare web services into Taverna, a generic scientific workflow platform.