The neXtProt knowledgebase in 2020: data, tools and usability improvements.

Journal: Nucleic acids research
Published Date: Jan 8, 2020

Abstract

The neXtProt knowledgebase (https://www.nextprot.org) is an integrative resource providing both data on human protein and the tools to explore these. In order to provide comprehensive and up-to-date data, we evaluate and add new data sets. We describe the incorporation of three new data sets that provide expression, function, protein-protein binary interaction, post-translational modifications (PTM) and variant information. New SPARQL query examples illustrating uses of the new data were added. neXtProt has continued to develop tools for proteomics. We have improved the peptide uniqueness checker and have implemented a new protein digestion tool. Together, these tools make it possible to determine which proteases can be used to identify trypsin-resistant proteins by mass spectrometry. In terms of usability, we have finished revamping our web interface and completely rewritten our API. Our SPARQL endpoint now supports federated queries. All the neXtProt data are available via our user interface, API, SPARQL endpoint and FTP site, including the new PEFF 1.0 format files. Finally, the data on our FTP site is now CC BY 4.0 to promote its reuse.

Authors

  • Monique Zahn-Zabal
    CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
  • Pierre-André Michel
    CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
  • Alain Gateau
    CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
  • Frédéric Nikitin
    CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
  • Mathieu Schaeffer
    CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
  • Estelle Audot
    CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
  • Pascale Gaudet
    Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, SIB Swiss Institute of Bioinformatics, 1 Rue Michel Servet, 1211 Geneva, Switzerland, Department of Medicine and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA, School of Information, University of South Florida, Tampa, FL, 33647, USA, Genomics Division, Lawrence Berkeley National Lab, 1 Cyclotron Rd., Berkeley, 94720 CA USA, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland, ETH Zurich, Department of Computer Science, Universitätstr. 19, 8092 Zürich, Switzerland, SIB Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zürich, Switzerland and University College London, Gower St, London WC1E 6BT, UK.
  • Paula D Duek
    CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
  • Daniel Teixeira
    CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
  • Valentine Rech de Laval
    CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
  • Kasun Samarasinghe
    CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
  • Amos Bairoch
    CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
  • Lydie Lane
    CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.

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