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

BioServices: a common Python package to access biological Web Services programmatically.

Thomas Cokelaer1, Dennis Pultz, Lea M Harder

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense 5230, Denmark, Translational Research Laboratory, Breast Cancer Unit, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), Gran via 199, L'Hospitalet del Llobregat, Barcelona 08908, Catalonia, Spain and Biomedical Research Institute of Girona, Girona 17007, Catalonia, Spain.

Bioinformatics (Oxford, England)
|September 26, 2013
PubMed
Summary
This summary is machine-generated.

BioServices offers a Python framework for accessing biological databases via Web Services. This simplifies building applications by integrating multiple bioinformatics resources like KEGG and UniProt programmatically.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Software Engineering

Background:

  • Numerous biological databases are accessible via web interfaces.
  • Programmatic access to these databases is often available through Web Services.
  • Integrating multiple bioinformatics web services into applications can be complex.

Purpose of the Study:

  • To develop a unified framework for accessing diverse bioinformatics web services.
  • To simplify the programmatic integration of multiple biological databases.
  • To facilitate the development of complex bioinformatics applications.

Main Methods:

  • Developed BioServices, a comprehensive Python framework.
  • Utilized object-oriented programming principles.
  • Designed to wrap Web Services based on Representational State Transfer (REST) or Simple Object Access Protocol (SOAP)/Web Services Description Language (WSDL).

Main Results:

  • BioServices provides programmatic access to major bioinformatics web services including KEGG, UniProt, BioModels, and ChEMBLdb.
  • The framework simplifies the integration of new web services.
  • Facilitates the creation of applications that leverage multiple bioinformatics data sources.

Conclusions:

  • BioServices streamlines access to bioinformatics web services.
  • The framework enhances the development of integrated bioinformatics applications.
  • Promotes efficient data retrieval and analysis in biological research.