EPA Science Inventory

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

Citation:

FOSTEL, J. M., L. BURGOON, C. ZWICKL, P. LORD, J C. CORTON, P. R. BUSHEL, M. CUNNINGHAM, L. FAN, S. W. EDWARDS, S. D. HESTER, J. STEVENS, W. TONG, M. WATERS, C. YANG, AND R. TENNANT. Toward a Checklist for Exchange and Interpretation of Data froma Toxicology Study. TOXICOLOGICAL SCIENCES. Society of Toxicology, 99(1):26-34, (2007).

Description:

With the advent of toxicogenomics came the need to share data across interdisciplinary teams and to deposit data associated with publications into public data repositories. Within a single institution, many variables associated with a study are standardized, for instance diet, animal strain, sex and age, method of euthanasia, housing conditions, dosing relative to circadian rhythm. As it becomes increasingly useful to share data across sites, this type of information is necessary to provide proper context for interpreting and understanding the data. At the moment, while many public initiatives are underway to define "minimal information" checklists, none represent toxicology or other disciplines with complex experimental designs by the inclusion of study organization and execution details. 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.

Purpose/Objective:

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.

URLs/Downloads:

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Record Details:

Record Type: DOCUMENT (JOURNAL/PEER REVIEWED JOURNAL)
Start Date: 09/01/2007
Completion Date: 09/01/2007
Record Last Revised: 05/15/2008
Record Created: 02/27/2007
Record Released: 02/27/2007
OMB Category: Other
Record ID: 165068

Organization:

U.S. ENVIRONMENTAL PROTECTION AGENCY

OFFICE OF RESEARCH AND DEVELOPMENT

NATIONAL HEALTH AND ENVIRONMENTAL EFFECTS RESEARCH LAB

ASSOCIATE DIRECTOR FOR HEALTH

IMMEDIATE OFFICE