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

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  • Thomas Cokelaer
    1 European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK, 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense 5230, Denmark, 3Translational 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 4Biomedical Research Institute of Girona, Girona 17007, Catalonia, Spain
  • Dennis Pultz
    1 European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK, 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense 5230, Denmark, 3Translational 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 4Biomedical Research Institute of Girona, Girona 17007, Catalonia, Spain
  • Lea M. Harder
    1 European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK, 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense 5230, Denmark, 3Translational 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 4Biomedical Research Institute of Girona, Girona 17007, Catalonia, Spain
  • Jordi Serra-Musach
    1 European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK, 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense 5230, Denmark, 3Translational 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 4Biomedical Research Institute of Girona, Girona 17007, Catalonia, Spain
  • Julio Saez-Rodriguez
    1 European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK, 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense 5230, Denmark, 3Translational 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 4Biomedical Research Institute of Girona, Girona 17007, Catalonia, Spain

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<jats:title>Abstract</jats:title> <jats:p>Motivation: Web interfaces provide access to numerous biological databases. Many can be accessed to in a programmatic way thanks to Web Services. Building applications that combine several of them would benefit from a single framework.</jats:p> <jats:p>Results: BioServices is a comprehensive Python framework that provides programmatic access to major bioinformatics Web Services (e.g. KEGG, UniProt, BioModels, ChEMBLdb). Wrapping additional Web Services based either on Representational State Transfer or Simple Object Access Protocol/Web Services Description Language technologies is eased by the usage of object-oriented programming.</jats:p> <jats:p>Availability and implementation: BioServices releases and documentation are available at http://pypi.python.org/pypi/bioservices under a GPL-v3 license.</jats:p> <jats:p>Contact:  cokelaer@ebi.ac.uk or bioservices@googlegroups.com</jats:p> <jats:p>Supplementary information:  Supplementary data are available at Bioinformatics online.</jats:p>

Journal

  • Bioinformatics

    Bioinformatics 29 (24), 3241-3242, 2013-09-23

    Oxford University Press (OUP)

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