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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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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.
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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.

Mentions: A major advance in the neXtProt functionality is the availability of a new advanced search system, designed to support the retrieval of proteins based on highly precise criteria taking into account the richness of the annotations and evidences. To implement this new functionality, we have converted the relational database into a graph representation using a subject-predicate-object model, RDF-based (Resource Description Framework). The graph representation is extremely powerful to navigate through the richness of the neXtProt data and to search it using the SPARQL query language. The advanced search is accessible at http://search.nextprot.org. An example query is shown in Figure 4.


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)

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

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

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.
Mentions: A major advance in the neXtProt functionality is the availability of a new advanced search system, designed to support the retrieval of proteins based on highly precise criteria taking into account the richness of the annotations and evidences. To implement this new functionality, we have converted the relational database into a graph representation using a subject-predicate-object model, RDF-based (Resource Description Framework). The graph representation is extremely powerful to navigate through the richness of the neXtProt data and to search it using the SPARQL query language. The advanced search is accessible at http://search.nextprot.org. An example query is shown in Figure 4.

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.

Show MeSH