NeXtProt: a Knowledge Platform for Human Proteins

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2011 Dec 6

PMID 22139911

Citations 69

Authors

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

Affiliations

Soon will be listed here.

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.

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References

Liebel U, Starkuviene V, Erfle H, Simpson J, Poustka A, Wiemann S . A microscope-based screening platform for large-scale functional protein analysis in intact cells. FEBS Lett. 2003; 554(3):394-8. DOI: 10.1016/s0014-5793(03)01197-9. View

Sewell W . MEDICAL SUBJECT HEADINGS IN MEDLARS. Bull Med Libr Assoc. 1964; 52:164-70. PMC: 198088. View

Sigal A, Danon T, Cohen A, Milo R, Geva-Zatorsky N, Lustig G . Generation of a fluorescently labeled endogenous protein library in living human cells. Nat Protoc. 2007; 2(6):1515-27. DOI: 10.1038/nprot.2007.197. View

Kelso J, Visagie J, Theiler G, Christoffels A, Bardien S, Smedley D . eVOC: a controlled vocabulary for unifying gene expression data. Genome Res. 2003; 13(6A):1222-30. PMC: 403650. DOI: 10.1101/gr.985203. View

Sayers E, Barrett T, Benson D, Bolton E, Bryant S, Canese K . Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2010; 39(Database issue):D38-51. PMC: 3013733. DOI: 10.1093/nar/gkq1172. View

Sigrist C, Cerutti L, de Castro E, Langendijk-Genevaux P, Bulliard V, Bairoch A . PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res. 2009; 38(Database issue):D161-6. PMC: 2808866. DOI: 10.1093/nar/gkp885. View

. Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res. 2010; 39(Database issue):D214-9. PMC: 3013648. DOI: 10.1093/nar/gkq1020. View

Altschul S, Gish W, Miller W, Myers E, Lipman D . Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. DOI: 10.1016/S0022-2836(05)80360-2. View

Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M . ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res. 2010; 39(Database issue):D1002-4. PMC: 3013660. DOI: 10.1093/nar/gkq1040. View

10.

Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, Forsberg M . Towards a knowledge-based Human Protein Atlas. Nat Biotechnol. 2010; 28(12):1248-50. DOI: 10.1038/nbt1210-1248. View

11.

Simpson J, Wellenreuther R, Poustka A, Pepperkok R, Wiemann S . Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. EMBO Rep. 2001; 1(3):287-92. PMC: 1083732. DOI: 10.1093/embo-reports/kvd058. View

12.

Pruitt K, Harrow J, Harte R, Wallin C, Diekhans M, Maglott D . The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res. 2009; 19(7):1316-23. PMC: 2704439. DOI: 10.1101/gr.080531.108. View

13.

Goel R, Muthusamy B, Pandey A, Keshava Prasad T . Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology. Mol Biotechnol. 2010; 48(1):87-95. DOI: 10.1007/s12033-010-9336-8. View

14.

Rose P, Beran B, Bi C, Bluhm W, Dimitropoulos D, Goodsell D . The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res. 2010; 39(Database issue):D392-401. PMC: 3013649. DOI: 10.1093/nar/gkq1021. View

15.

Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1):25-9. PMC: 3037419. DOI: 10.1038/75556. View

16.

Mejino Jr J, Agoncillo A, Rickard K, Rosse C . Representing complexity in part-whole relationships within the Foundational Model of Anatomy. AMIA Annu Symp Proc. 2004; :450-4. PMC: 1480337. View

17.

Bairoch A . The ENZYME database in 2000. Nucleic Acids Res. 1999; 28(1):304-5. PMC: 102465. DOI: 10.1093/nar/28.1.304. View

18.

Legrain P, Aebersold R, Archakov A, Bairoch A, Bala K, Beretta L . The human proteome project: current state and future direction. Mol Cell Proteomics. 2011; 10(7):M111.009993. PMC: 3134076. DOI: 10.1074/mcp.M111.009993. View

19.

Orchard S, Hoogland C, Bairoch A, Eisenacher M, Kraus H, Binz P . Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands. Proteomics. 2009; 9(3):499-501. DOI: 10.1002/pmic.200800838. View

20.

Morgat A, Coissac E, Coudert E, Axelsen K, Keller G, Bairoch A . UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res. 2011; 40(Database issue):D761-9. PMC: 3245108. DOI: 10.1093/nar/gkr1023. View