Literature DB >> 18065433

The HUPO proteomics standards initiative--easing communication and minimizing data loss in a changing world.

Sandra Orchard1, Henning Hermjakob.   

Abstract

The amount of data currently being generated by proteomics laboratories around the world is increasing exponentially, making it ever more critical that scientists are able to exchange, compare and retrieve datasets when re-evaluation of their original conclusions becomes important. Only a fraction of this data is published in the literature and important information is being lost every day as data formats become obsolete. The Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) was tasked with the creation of data standards and interchange formats to allow both the exchange and storage of such data irrespective of the hardware and software from which it was generated. This article will provide an update on the work of this group, the creation and implementation of these standards and the standards-compliant data repositories being established as result of their efforts.

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Year:  2007        PMID: 18065433     DOI: 10.1093/bib/bbm061

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN: 1467-5463            Impact factor:   11.622


  11 in total

1.  Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology.

Authors:  Renu Goel; Babylakshmi Muthusamy; Akhilesh Pandey; T S Keshava Prasad
Journal:  Mol Biotechnol       Date:  2011-05       Impact factor: 2.695

Review 2.  Minireview: progress and challenges in proteomics data management, sharing, and integration.

Authors:  Lauren B Becnel; Neil J McKenna
Journal:  Mol Endocrinol       Date:  2012-08-17

Review 3.  Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis.

Authors:  Renu Goel; H C Harsha; Akhilesh Pandey; T S Keshava Prasad
Journal:  Mol Biosyst       Date:  2011-12-08

4.  Protein interaction data curation: the International Molecular Exchange (IMEx) consortium.

Authors:  Sandra Orchard; Samuel Kerrien; Sara Abbani; Bruno Aranda; Jignesh Bhate; Shelby Bidwell; Alan Bridge; Leonardo Briganti; Fiona S L Brinkman; Fiona Brinkman; Gianni Cesareni; Andrew Chatr-aryamontri; Emilie Chautard; Carol Chen; Marine Dumousseau; Johannes Goll; Robert E W Hancock; Robert Hancock; Linda I Hannick; Igor Jurisica; Jyoti Khadake; David J Lynn; Usha Mahadevan; Livia Perfetto; Arathi Raghunath; Sylvie Ricard-Blum; Bernd Roechert; Lukasz Salwinski; Volker Stümpflen; Mike Tyers; Peter Uetz; Ioannis Xenarios; Henning Hermjakob
Journal:  Nat Methods       Date:  2012-04       Impact factor: 28.547

5.  Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol.

Authors:  Sébastien Gallien; Emmanuel Perrodou; Christine Carapito; Caroline Deshayes; Jean-Marc Reyrat; Alain Van Dorsselaer; Olivier Poch; Christine Schaeffer; Odile Lecompte
Journal:  Genome Res       Date:  2008-10-27       Impact factor: 9.043

6.  XML-based approaches for the integration of heterogeneous bio-molecular data.

Authors:  Marco Mesiti; Ernesto Jiménez-Ruiz; Ismael Sanz; Rafael Berlanga-Llavori; Paolo Perlasca; Giorgio Valentini; David Manset
Journal:  BMC Bioinformatics       Date:  2009-10-15       Impact factor: 3.169

7.  OLS dialog: an open-source front end to the ontology lookup service.

Authors:  Harald Barsnes; Richard G Côté; Ingvar Eidhammer; Lennart Martens
Journal:  BMC Bioinformatics       Date:  2010-01-17       Impact factor: 3.169

Review 8.  Proteomics and systems biology for understanding diabetic nephropathy.

Authors:  Jonathan M Starkey; Ronald G Tilton
Journal:  J Cardiovasc Transl Res       Date:  2012-05-12       Impact factor: 4.132

Review 9.  Data standards for Omics data: the basis of data sharing and reuse.

Authors:  Stephen A Chervitz; Eric W Deutsch; Dawn Field; Helen Parkinson; John Quackenbush; Phillipe Rocca-Serra; Susanna-Assunta Sansone; Christian J Stoeckert; Chris F Taylor; Ronald Taylor; Catherine A Ball
Journal:  Methods Mol Biol       Date:  2011

10.  Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

Authors:  Peter B McGarvey; Hongzhan Huang; Raja Mazumder; Jian Zhang; Yongxing Chen; Chengdong Zhang; Stephen Cammer; Rebecca Will; Margie Odle; Bruno Sobral; Margaret Moore; Cathy H Wu
Journal:  PLoS One       Date:  2009-09-25       Impact factor: 3.240

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