Skip Navigation


ToxSci Advance Access originally published online on April 17, 2007
Toxicological Sciences 2007 99(1):26-34; doi:10.1093/toxsci/kfm090
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supplementary Data
Right arrow All Versions of this Article:
99/1/26    most recent
kfm090v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (1)
Right arrowRequest Permissions
Right arrow Disclaimer
Google Scholar
Right arrow Articles by Fostel, J. M.
Right arrow Articles by Tennant, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Fostel, J. M.
Right arrow Articles by Tennant, R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published by Oxford University Press 2007.

Toward a Checklist for Exchange and Interpretation of Data from a Toxicology Study

Jennifer M. Fostel*,1, Lyle Burgoon{dagger}, Craig Zwickl{ddagger}, Peter Lord§, J. Christopher Corton, Pierre R. Bushel|, Michael Cunningham||, Liju Fan|||, Stephen W. Edwards, Susan Hester, James Stevens{ddagger}, Weida Tong#, Michael Waters**, ChiHae Yang{dagger}{dagger} and Raymond Tennant||

* NIEHS, LMIT ITSS Contract, Research Triangle Park, North Carolina 27709-2233 {dagger} Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 {ddagger} Lilly Research Laboratory, Greenfield, Indiana 46140 § Johnson and Johnson PRD, Raritan, New Jersey 08869 National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711 | NIEHS, Research Triangle Park, North Carolina 27709-2233 || National Toxicology Program, Research Triangle Park, North Carolina 27709 ||| Ontology Workshop, LLC, Columbia, Maryland 21045-9998 # National Center for Toxicological Research, Jefferson, Arkansas 72079 ** Integrated Life Sciences, Research Triangle Park, North Carolina 27709 {dagger}{dagger} Leadscope, Columbus, Ohio 43212

1 To whom correspondence should be addressed at NIEHS, MD F1-05, PO Box 12233, 111 Alexander Drive, Research Triangle Park, NC, 27709-2233. E-mail: fostel{at}niehs.nih.gov.

Received February 13, 2007; accepted April 3, 2007


  Abstract

Data from toxicology and toxicogenomics studies are valuable, and can be combined for meta-analysis using public data repositories such as Chemical Effects in Biological Systems Knowledgebase, ArrayExpress, and Gene Expression Omnibus. In order to fully utilize the data for secondary analysis, it is necessary to have a description of the study and good annotation of the accompanying data. This study annotation permits sophisticated cross-study comparison and analysis, and allows data from comparable subjects to be identified and fully understood. The Minimal Information About a Microarray Experiment Standard was proposed to permit deposition and sharing of microarray data. We propose the first step toward an analogous standard for a toxicogenomics/toxicology study, by describing a checklist of information that best practices would suggest be included with the study data. When the information in this checklist is deposited together with the study data, the checklist information helps the public explore the study data in context of time, or identify data from similarly treated subjects, and also explore/identify potential sources of experimental variability. The proposed checklist summarizes useful information to include when sharing study data for publication, deposition into a database, or electronic exchange with collaborators. It is not a description of how to carry out an experiment, but a definition of how to describe an experiment. It is anticipated that once a toxicology checklist is accepted and put into use, then toxicology databases can be configured to require and output these fields, making it straightforward to annotate data for interpretation by others.

Key Words: Toxicogenomics; MIAME; Data integration; Database.

This manuscript has been reviewed and approved for publication by the Environmental Protection Agency but does not necessarily reflect the views of the Agency. Mention of trade names or commercial products does not constitute endorsement or recommendations for use.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
M. Waters, S. Stasiewicz, B. Alex Merrick, K. Tomer, P. Bushel, R. Paules, N. Stegman, G. Nehls, K. J. Yost, C. H. Johnson, et al.
CEBS Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D892 - D900.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.