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

Article Article scientifique Article The neXtProt knowledgebase in 2020: data, tools and usability improvements eng 2020 author Zahn Monique 766292 author Michel Pierre-André Albert 72788 author Gateau Alain 114432 author Nikitin Frédéric 545323 author Schaeffer Mathieu 836265 author Audot Estelle 930482 author Gaudet Pascale 739115 author Duek Paula Debora 547123 author Teixeira Daniel author Rech De Laval Valentine 831162 author Wijesiriwardana Kasun 759244 author Bairoch Amos Marc 0000-0003-2826-6444 21964 author Lane Lydie 0000-0002-9818-3030 639317 D328-D334 10.1093/nar/gkz995 31724716 0305-1048 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. Dewey 616 54 Département de microbiologie et médecine moléculaire 21B false 57 Calipho 80 Nucleic Acids Research 48 D1 4ddd2464-7ba4-4bdc-a223-6b9c1d1bea0b Article (Published version) Public nar2020.pdf 2012665 application/pdf CC BY openAccess Faculté de médecine / Section de médecine fondamentale / Département de microbiologie et médecine moléculaire

Title	Published in	Access level	OA Policy	Year	Views	Downloads

The neXtProt knowledgebase in 2020: data, tools and usability improvements	Nucleic Acids Research			2020	516	658

Archive ouverte UNIGE

Audot, Estelle