Literature DB >> 18629184

Standardization Initiatives in the (eco)toxicogenomics domain: a review.

Susanna Assunta Sansone1, Norman Morrison, Philippe Rocca-Serra, Jennifer Fostel.   

Abstract

The purpose of this document is to provide readers with a resource of different ongoing standardization efforts within the 'omics' (genomic, proteomics, metabolomics) and related communities, with particular focus on toxicological and environmental applications. The review includes initiatives within the research community as well as in the regulatory arena. It addresses data management issues (format and reporting structures for the exchange of information) and database interoperability, highlighting key objectives, target audience and participants. A considerable amount of work still needs to be done and, ideally, collaboration should be optimized and duplication and incompatibility should be avoided where possible. The consequence of failing to deliver data standards is an escalation in the burden and cost of data management tasks.

Entities:  

Year:  2004        PMID: 18629184      PMCID: PMC2447477          DOI: 10.1002/cfg.447

Source DB:  PubMed          Journal:  Comp Funct Genomics        ISSN: 1531-6912


  15 in total

1.  Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Authors:  A Brazma; P Hingamp; J Quackenbush; G Sherlock; P Spellman; C Stoeckert; J Aach; W Ansorge; C A Ball; H C Causton; T Gaasterland; P Glenisson; F C Holstege; I F Kim; V Markowitz; J C Matese; H Parkinson; A Robinson; U Sarkans; S Schulze-Kremer; J Stewart; R Taylor; J Vilo; M Vingron
Journal:  Nat Genet       Date:  2001-12       Impact factor: 38.330

2.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.

Authors:  Ron Edgar; Michael Domrachev; Alex E Lash
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

Review 3.  Microarray databases: standards and ontologies.

Authors:  Christian J Stoeckert; Helen C Causton; Catherine A Ball
Journal:  Nat Genet       Date:  2002-12       Impact factor: 38.330

4.  Standards for microarray data.

Authors:  Catherine A Ball; Gavin Sherlock; Helen Parkinson; Philippe Rocca-Sera; Catherine Brooksbank; Helen C Causton; Duccio Cavalieri; Terry Gaasterland; Pascal Hingamp; Frank Holstege; Martin Ringwald; Paul Spellman; Christian J Stoeckert; Jason E Stewart; Ronald Taylor; Alvis Brazma; John Quackenbush
Journal:  Science       Date:  2002-10-18       Impact factor: 47.728

5.  CIBEX: center for information biology gene expression database.

Authors:  Kazuho Ikeo; Jun Ishi-i; Takurou Tamura; Takashi Gojobori; Yoshio Tateno
Journal:  C R Biol       Date:  2003 Oct-Nov       Impact factor: 1.583

6.  ArrayExpress--a public repository for microarray gene expression data at the EBI.

Authors:  Alvis Brazma; Helen Parkinson; Ugis Sarkans; Mohammadreza Shojatalab; Jaak Vilo; Niran Abeygunawardena; Ele Holloway; Misha Kapushesky; Patrick Kemmeren; Gonzalo Garcia Lara; Ahmet Oezcimen; Philippe Rocca-Serra; Susanna-Assunta Sansone
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

7.  The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.

Authors:  Henning Hermjakob; Luisa Montecchi-Palazzi; Gary Bader; Jérôme Wojcik; Lukasz Salwinski; Arnaud Ceol; Susan Moore; Sandra Orchard; Ugis Sarkans; Christian von Mering; Bernd Roechert; Sylvain Poux; Eva Jung; Henning Mersch; Paul Kersey; Michael Lappe; Yixue Li; Rong Zeng; Debashis Rana; Macha Nikolski; Holger Husi; Christine Brun; K Shanker; Seth G N Grant; Chris Sander; Peer Bork; Weimin Zhu; Akhilesh Pandey; Alvis Brazma; Bernard Jacq; Marc Vidal; David Sherman; Pierre Legrain; Gianni Cesareni; Ioannis Xenarios; David Eisenberg; Boris Steipe; Chris Hogue; Rolf Apweiler
Journal:  Nat Biotechnol       Date:  2004-02       Impact factor: 54.908

Review 8.  Toxicogenomics in risk assessment: an overview of an HESI collaborative research program.

Authors:  William Pennie; Syril D Pettit; Peter G Lord
Journal:  Environ Health Perspect       Date:  2004-03       Impact factor: 9.031

Review 9.  ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research.

Authors:  Weida Tong; Xiaoxi Cao; Stephen Harris; Hongmei Sun; Hong Fang; James Fuscoe; Angela Harris; Huixiao Hong; Qian Xie; Roger Perkins; Leming Shi; Dan Casciano
Journal:  Environ Health Perspect       Date:  2003-11       Impact factor: 9.031

10.  Design and implementation of microarray gene expression markup language (MAGE-ML).

Authors:  Paul T Spellman; Michael Miller; Jason Stewart; Charles Troup; Ugis Sarkans; Steve Chervitz; Derek Bernhart; Gavin Sherlock; Catherine Ball; Marc Lepage; Marcin Swiatek; W L Marks; Jason Goncalves; Scott Markel; Daniel Iordan; Mohammadreza Shojatalab; Angel Pizarro; Joe White; Robert Hubley; Eric Deutsch; Martin Senger; Bruce J Aronow; Alan Robinson; Doug Bassett; Christian J Stoeckert; Alvis Brazma
Journal:  Genome Biol       Date:  2002-08-23       Impact factor: 13.583

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  2 in total

1.  Meeting report: Validation of toxicogenomics-based test systems: ECVAM-ICCVAM/NICEATM considerations for regulatory use.

Authors:  Raffaella Corvi; Hans-Jürgen Ahr; Silvio Albertini; David H Blakey; Libero Clerici; Sandra Coecke; George R Douglas; Laura Gribaldo; John P Groten; Bernd Haase; Karen Hamernik; Thomas Hartung; Tohru Inoue; Ian Indans; Daniela Maurici; George Orphanides; Diana Rembges; Susanna-Assunta Sansone; Jason R Snape; Eisaku Toda; Weida Tong; Joost H van Delft; Brenda Weis; Leonard M Schechtman
Journal:  Environ Health Perspect       Date:  2006-03       Impact factor: 9.031

2.  Standardizing the standards.

Authors:  John Quackenbush
Journal:  Mol Syst Biol       Date:  2006-02-21       Impact factor: 11.429

  2 in total

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