- The neXtProt knowledgebase on human proteins: 2017 update. [PMID: 27899619]
Pascale Gaudet, Pierre-André Michel, Monique Zahn-Zabal, Aurore Britan, Isabelle Cusin, Marcin Domagalski, Paula D Duek, Alain Gateau, Anne Gleizes, Valérie Hinard, Valentine Rech de Laval, JinJin Lin, Frederic Nikitin, Mathieu Schaeffer, Daniel Teixeira, Lydie Lane, Amos Bairoch
Nucleic acids research 2017:45(D1)
0 Citations (Google Scholar as of 2017-02-13)
Abstract: The neXtProt human protein knowledgebase (https://www.nextprot.org) continues to add new content and tools, with a focus on proteomics and genetic variation data. neXtProt now has proteomics data for over 85% of the human proteins, as well as new tools tailored to the proteomics community.Moreover, the neXtProt release 2016-08-25 includes over 8000 phenotypic observations for over 4000 variations in a number of genes involved in hereditary cancers and channelopathies. These changes are presented in the current neXtProt update. All of the neXtProt data are available via our user interface and FTP site. We also provide an API access and a SPARQL endpoint for more technical applications. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
- The neXtProt knowledgebase on human proteins: current status. [PMID: 25593349]
Pascale Gaudet, Pierre-André Michel, Monique Zahn-Zabal, Isabelle Cusin, Paula D Duek, Olivier Evalet, Alain Gateau, Anne Gleizes, Mario Pereira, Daniel Teixeira, Ying Zhang, Lydie Lane, Amos Bairoch
Nucleic acids research 2015:43(Database issue)
48 Citations (Google Scholar as of 2017-02-13)
Abstract: neXtProt (http://www.nextprot.org) is a human protein-centric knowledgebase developed at the SIB Swiss Institute of Bioinformatics. Focused solely on human proteins, neXtProt aims to provide a state of the art resource for the representation of human biology by capturing a wide range of data, precise annotations, fully traceable data provenance and a web interface which enables researchers to find and view information in a comprehensive manner. Since the introductory neXtProt publication, significant advances have been made on three main aspects: the representation of proteomics data, an extended representation of human variants and the development of an advanced search capability built around semantic technologies. These changes are presented in the current neXtProt update. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
- neXtProt: organizing protein knowledge in the context of human proteome projects. [PMID: 23205526]
Pascale Gaudet, Ghislaine Argoud-Puy, Isabelle Cusin, Paula Duek, Olivier Evalet, Alain Gateau, Anne Gleizes, Mario Pereira, Monique Zahn-Zabal, Catherine Zwahlen, Amos Bairoch, Lydie Lane
Journal of proteome research 2013:12(1)
86 Citations (Google Scholar as of 2017-02-13)
Abstract: About 5000 (25%) of the ~20400 human protein-coding genes currently lack any experimental evidence at the protein level. For many others, there is only little information relative to their abundance, distribution, subcellular localization, interactions, or cellular functions. The aim of the HUPO Human Proteome Project (HPP, www.thehpp.org ) is to collect this information for every human protein. HPP is based on three major pillars: mass spectrometry (MS), antibody/affinity capture reagents (Ab), and bioinformatics-driven knowledge base (KB). To meet this objective, the Chromosome-Centric Human Proteome Project (C-HPP) proposes to build this catalog chromosome-by-chromosome ( www.c-hpp.org ) by focusing primarily on proteins that currently lack MS evidence or Ab detection. These are termed "missing proteins" by the HPP consortium. The lack of observation of a protein can be due to various factors including incorrect and incomplete gene annotation, low or restricted expression, or instability. neXtProt ( www.nextprot.org ) is a new web-based knowledge platform specific for human proteins that aims to complement UniProtKB/Swiss-Prot ( www.uniprot.org ) with detailed information obtained from carefully selected high-throughput experiments on genomic variation, post-translational modifications, as well as protein expression in tissues and cells. This article describes how neXtProt contributes to prioritize C-HPP efforts and integrates C-HPP results with other research efforts to create a complete human proteome catalog.
- neXtProt: a knowledge platform for human proteins. [PMID: 22139911]
Lydie Lane, Ghislaine Argoud-Puy, Aurore Britan, Isabelle Cusin, Paula D Duek, Olivier Evalet, Alain Gateau, Pascale Gaudet, Anne Gleizes, Alexandre Masselot, Catherine Zwahlen, Amos Bairoch
Nucleic acids research 2012:40(Database issue)
103 Citations (Google Scholar as of 2017-02-13)
Abstract: neXtProt (http://www.nextprot.org/) is a new human protein-centric knowledge platform. Developed at the Swiss Institute of Bioinformatics (SIB), it aims to help researchers answer questions relevant to human proteins. To achieve this goal, neXtProt is built on a corpus containing both curated knowledge originating from the UniProtKB/Swiss-Prot knowledgebase and carefully selected and filtered high-throughput data pertinent to human proteins. This article presents an overview of the database and the data integration process. We also lay out the key future directions of neXtProt that we consider the necessary steps to make neXtProt the one-stop-shop for all research projects focusing on human proteins.