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

Monique Zahn-Zabal1, Pierre-André Michel1, Alain Gateau1

  • 1CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.

Nucleic Acids Research
|November 15, 2019
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Summary
This summary is machine-generated.

The neXtProt knowledgebase now offers expanded human protein data, including expression, function, and interactions. Enhanced tools and a revamped interface improve proteomics research accessibility and data reuse.

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Molecular Biology

Background:

  • The neXtProt knowledgebase is a crucial resource for human protein data and exploration tools.
  • Continuous updates are essential to maintain comprehensive and current information.
  • Integrating diverse datasets enhances the depth and breadth of protein information.

Purpose of the Study:

  • To describe the incorporation of new datasets into neXtProt.
  • To highlight advancements in neXtProt's proteomics tools and usability features.
  • To promote wider data accessibility and reuse.

Main Methods:

  • Incorporation of new datasets covering protein expression, function, interactions, post-translational modifications (PTMs), and variants.
  • Development and improvement of proteomics tools, including a peptide uniqueness checker and a protein digestion tool.
  • Revamping the web interface and API, enhancing the SPARQL endpoint, and updating data file formats (PEFF 1.0).

Main Results:

  • Three new datasets providing expression, function, protein-protein interactions, PTMs, and variant information have been added.
  • Improved proteomics tools enable identification of trypsin-resistant proteins for mass spectrometry.
  • A revamped web interface, rewritten API, and enhanced SPARQL endpoint improve user experience and data querying capabilities.

Conclusions:

  • neXtProt has significantly expanded its human protein data and improved its analytical tools.
  • Enhanced usability and data accessibility, including CC BY 4.0 licensing, promote broader research applications.
  • These updates solidify neXtProt's role as a leading resource for proteomics research.