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. 2004 Dec;5(8):633–641. doi: 10.1002/cfg.447

Standardization Initiatives in the (eco)toxicogenomics Domain: A Review

Susanna Assunta Sansone 1,, Norman Morrison 2, Philippe Rocca-Serra 1, Jennifer Fostel 3
PMCID: PMC2447477  PMID: 18629184

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.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Ball Catherine A., Sherlock Gavin, Parkinson Helen, Rocca-Sera Philippe, Brooksbank Catherine, Causton Helen C., Cavalieri Duccio, Gaasterland Terry, Hingamp Pascal, Holstege Frank. Standards for microarray data. Science. 2002 Oct 18;298(5593):539–539. doi: 10.1126/science.298.5593.539b. [DOI] [PubMed] [Google Scholar]
  2. Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C. A., Causton H. C. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001 Dec;29(4):365–371. doi: 10.1038/ng1201-365. [DOI] [PubMed] [Google Scholar]
  3. Brazma Alvis, Parkinson Helen, Sarkans Ugis, Shojatalab Mohammadreza, Vilo Jaak, Abeygunawardena Niran, Holloway Ele, Kapushesky Misha, Kemmeren Patrick, Lara Gonzalo Garcia. ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 2003 Jan 1;31(1):68–71. doi: 10.1093/nar/gkg091. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Edgar Ron, Domrachev Michael, Lash Alex E. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002 Jan 1;30(1):207–210. doi: 10.1093/nar/30.1.207. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Hermjakob Henning, Montecchi-Palazzi Luisa, Bader Gary, Wojcik Jérôme, Salwinski Lukasz, Ceol Arnaud, Moore Susan, Orchard Sandra, Sarkans Ugis, von Mering Christian. The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol. 2004 Feb;22(2):177–183. doi: 10.1038/nbt926. [DOI] [PubMed] [Google Scholar]
  6. Ikeo Kazuho, Ishi-i Jun, Tamura Takurou, Gojobori Takashi, Tateno Yoshio. CIBEX: center for information biology gene expression database. C R Biol. 2003 Oct-Nov;326(10-11):1079–1082. doi: 10.1016/j.crvi.2003.09.034. [DOI] [PubMed] [Google Scholar]
  7. Mattes William B., Pettit Syril D., Sansone Susanna-Assunta, Bushel Pierre R., Waters Michael D. Database development in toxicogenomics: issues and efforts. Environ Health Perspect. 2004 Mar;112(4):495–505. doi: 10.1289/ehp.6697. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Pennie William, Pettit Syril D., Lord Peter G. Toxicogenomics in risk assessment: an overview of an HESI collaborative research program. Environ Health Perspect. 2004 Mar;112(4):417–419. doi: 10.1289/ehp.6674. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Quackenbush John. Data standards for 'omic' science. Nat Biotechnol. 2004 May;22(5):613–614. doi: 10.1038/nbt0504-613. [DOI] [PubMed] [Google Scholar]
  10. Spellman Paul T., Miller Michael, Stewart Jason, Troup Charles, Sarkans Ugis, Chervitz Steve, Bernhart Derek, Sherlock Gavin, Ball Catherine, Lepage Marc. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol. 2002 Aug 23;3(9):RESEARCH0046–RESEARCH0046. doi: 10.1186/gb-2002-3-9-research0046. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Stoeckert Christian J., Jr, Causton Helen C., Ball Catherine A. Microarray databases: standards and ontologies. Nat Genet. 2002 Dec;32 (Suppl):469–473. doi: 10.1038/ng1028. [DOI] [PubMed] [Google Scholar]
  12. Stoeckert Christian J., Jr, Parkinson Helen. The MGED ontology: a framework for describing functional genomics experiments. Comp Funct Genomics. 2003;4(1):127–132. doi: 10.1002/cfg.234. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Tong Weida, Cao Xiaoxi, Harris Stephen, Sun Hongmei, Fang Hong, Fuscoe James, Harris Angela, Hong Huixiao, Xie Qian, Perkins Roger. ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research. Environ Health Perspect. 2003 Nov;111(15):1819–1826. doi: 10.1289/ehp.6497. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Waters Michael D., Fostel Jennifer M. Toxicogenomics and systems toxicology: aims and prospects. Nat Rev Genet. 2004 Dec;5(12):936–948. doi: 10.1038/nrg1493. [DOI] [PubMed] [Google Scholar]
  15. Xirasagar Sandhya, Gustafson Scott, Merrick B. Alex, Tomer Kenneth B., Stasiewicz Stanley, Chan Denny D., Yost Kenneth J., 3rd, Yates John R., 3rd, Sumner Susan, Xiao Nianqing. CEBS object model for systems biology data, SysBio-OM. Bioinformatics. 2004 Mar 25;20(13):2004–2015. doi: 10.1093/bioinformatics/bth189. [DOI] [PubMed] [Google Scholar]

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