Toward a checklist for exchange and interpretation of data from a toxicology study.
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.
Fostel
Jennifer M
JM
NIEHS, LMIT ITSS Contract, Research Triangle Park, North Carolina 27709-2233, USA. fostel@niehs.nih.gov
Burgoon
Lyle
L
Zwickl
Craig
C
Lord
Peter
P
Corton
J Christopher
JC
Bushel
Pierre R
PR
Cunningham
Michael
M
Fan
Liju
L
Edwards
Stephen W
SW
Hester
Susan
S
Stevens
James
J
Tong
Weida
W
Waters
Michael
M
Yang
ChiHae
C
Tennant
Raymond
R
D000818:Animals; D003625:Data Collection; D003626:Data Display; D003627:Data Interpretation, Statistical; D030541:Databases, Genetic; D015201:Meta-Analysis as Topic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods / Q000706:statistics & numerical data; D012984:Software; D018675:Toxicity Tests / Q000379:methods* / Q000706:statistics & numerical data