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

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.

Figure 1.

Tabular view showing the expression data for insulin (NX_P01308). Expression data at the mRNA and protein level are displayed in the same semi-quantitative manner for easier comparison. Four levels of expression (undetected, low, medium, high) are possible. Mousing-over the data point displays the expression level textually.

Figure 2.

Allele frequency information in the Sequence view for BRCA1 (NX_P38398) variants. To find a gnomAD variant, search in the feature table with the gnomAD ID. A link to the corresponding variant in gnomAD is found in the description of the variant and the evidence. The allele frequency, with the allele count and allele number in brackets, as well as the homozygote count, are displayed in the evidence.

Figure 3.

Protein digestion tool. (A) Input form requiring the neXtProt isoform accession number for the protein to be digested. Default digestion parameters (maximum number of miscleavages, minimum peptide length and maximum peptide length) can be modified by the user. (B) Peptide count and unique peptide count for the digestion with 27 proteases or conditions. Select a protease to see the peptides obtained. (C) Table displaying information about the peptides obtained with the selected digestion conditions. The peptide sequence, length, number of missed cleavages, position in the sequence, whether the peptide is unique or not (without taking into account variants) and whether the peptide is found in neXtProt, as a natural and synthetic (SRM peptide) are displayed. A link to the neXtProt Peptide view of the entry is provided.

Figure 4.

Federated SPARQL query examples. Screenshot showing all queries tagged ‘federated’ in the neXtProt SNORQL interface.