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The neXtProt knowledgebase on human proteins: current status.

Gaudet P, Michel PA, Zahn-Zabal M, Cusin I, Duek PD, Evalet O, Gateau A, Gleizes A, Pereira M, Teixeira D, Zhang Y, Lane L, Bairoch A - Nucleic Acids Res. (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland, 1211 Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland, 1211 pascale.gaudet@isb-sib.ch.

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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).
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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).

Mentions: We have completely restructured the neXtProt data model and infrastructure. The objective of these changes was to allow neXtProt users to precisely extract information that they are interested in; to manage list of proteins (originating from the results of searches, or created by users); and build analysis tools on top of neXtProt. Figure 2 gives an overview of the new neXtProt architecture and the technologies used.


The neXtProt knowledgebase on human proteins: current status.

Gaudet P, Michel PA, Zahn-Zabal M, Cusin I, Duek PD, Evalet O, Gateau A, Gleizes A, Pereira M, Teixeira D, Zhang Y, Lane L, Bairoch A - Nucleic Acids Res. (2015)

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).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383972&req=5

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).
Mentions: We have completely restructured the neXtProt data model and infrastructure. The objective of these changes was to allow neXtProt users to precisely extract information that they are interested in; to manage list of proteins (originating from the results of searches, or created by users); and build analysis tools on top of neXtProt. Figure 2 gives an overview of the new neXtProt architecture and the technologies used.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland, 1211 Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland, 1211 pascale.gaudet@isb-sib.ch.

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