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ToxSci Advance Access published online on April 17, 2007
Toxicological Sciences, doi:10.1093/toxsci/kfm090
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Published by Oxford University Press 2007.

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

Jennifer M. Fostel*, Lyle Burgoon{dagger}, Craig Zwickl{ddagger}, Peter Lord§, J. Christopher Corton, Pierre R. Bushellll, Michael Cunninghamllll, Liju Fan#, Stephen W. Edwards, Susan Hester, James Stevens{ddagger}, Weida Tong**, Michael Waters{dagger}{dagger}, ChiHae Yanga and Raymond Tennantlll

* NIEHS, LMIT ITSS Contract, Research Triangle Park, NC, 27709-2233, USA {dagger} Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA. Burgoonl{at}msu.edu {ddagger} Lilly Research Laboratory, Greenfield, IN 46140, USA. Stevens_James_L{at}Lilly.com; Zwickl_Craig_M{at}Lilly.com § Johnson and Johnson PRD, Raritan, NJ 08869, USA. PLord{at}prdus.jnj.com National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA Corton.Chris{at}epamail.epa.gov; Edwards.Stephen{at}epamail.epa.gov; Hester.Susan{at}epamail.epa.gov lll NIEHS, Research Triangle Park, NC 27709-2233. Bushel{at}niehs.nih.gov; Tennant{at}niehs.nih.gov llll National Toxicology Program, Research Triangle Park, NC 27709. Cunning1{at}niehs.nih.gov # Ontology Workshop, LLC, Columbia, MD 21045-9998, USA. Liju.Fan{at}gmail.com ** National Center for Toxicological Research, Jefferson, AR 72079, USA. Weida.Tong{at}fda.hhs.gov {dagger}{dagger} Integrated Life Sciences, Research Triangle Park, NC, 27709, USA. MWaters{at}ils-inc.com a Leadscope, Columbus, Ohio 43212 USA. CYang{at}leadscope.com

Corresponding Author: fostel{at}niehs.nih.gov

Received February 13, 2007; revision received April 2, 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 CEBS, ArrayExpress and GEO. 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 (MIAME) Standard was proposed to permit deposition and sharing of microarray data. We propose the first step towards 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.


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