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. 2015 Jan;43(Database issue):D764-70.
doi: 10.1093/nar/gku1178.

The neXtProt knowledgebase on human proteins: current status

Pascale Gaudet  1 , Pierre-André Michel  2 , Monique Zahn-Zabal  2 , Isabelle Cusin  2 , Paula D Duek  2 , Olivier Evalet  2 , Alain Gateau  2 , Anne Gleizes  2 , Mario Pereira  2 , Daniel Teixeira  2 , Ying Zhang  2 , Lydie Lane  3 , Amos Bairoch  3
Affiliations

The neXtProt knowledgebase on human proteins: current status

Pascale Gaudet et al. Nucleic Acids Res. 2015 Jan.

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.

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Figures

Figure 1.
Figure 1.
The neXtProt proteomics view displays a new track for ‘SRM Peptides’ that have been chemically synthesized and validated by SRMAtlas. As for the other views displaying sequences, the graphical view, the table and the sequence are linked together, so that upon selection of a peptide in the graphical view, it is highlighted in the table and in the sequence. As shown by the peptide selected above, some SRM peptides correspond to natural peptides identified in biological samples; in this case they are shown twice, with their respective evidences.
Figure 2.
Figure 2.
The new neXtProt infrastructure. neXtProt implements the following software and packages: Spring: open source web application over Java (spring.io); Spring JDBC templates: thin API between database and data objects (http://docs.spring.io/spring/docs/3.0.x/spring-framework-reference/html/jdbc.html); PostgreSQL: database where sequences, annotations, evidences and terms, as well as user resources (profiles, saved lists and queries) are stored (http://www.postgresql.org); Lucene/solr: full-text search engine for simple search queries (http://lucene.apache.org and http://lucene.apache.org/solr); Jena: graph search API for complex search queries (http://jena.apache.org); and Virtuoso: to store RDF data and perform complex SPARQL search queries (http://virtuoso.openlinksw.com).
Figure 3.
Figure 3.
The neXtProt list manager can be used to save lists, make operations such as combining them, and export the entries contained in a list. The full entries can be exported, or only certain data, such as accession numbers, the overview, the general annotations, etc.
Figure 4.
Figure 4.
Example of a neXtProt advanced search. This query retrieves entries corresponding to proteins having a PDZ domain and that interact with at least one protein expressed in the brain. The query returns 129 entries. Results can be sorted according to gene name, protein name, protein family name, chromosome, accession number or protein length. The results can also be saved as list, and that list exported in different formats such as text, XML or JSON.
Figure 5.
Figure 5.
Examples of SPARQL queries available in the advanced search page. The examples cover a wide range of different queries and many incorporate counts of objects (for example, retrieve proteins having three disulfide bonds).
See this image and copyright information in PMC

References

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