thology, toxicology, and chemical compound nomenclature). The use of controlled vocabularies is needed to enable database queries and automated data analysis.

MIAME/Tox guidelines have been adopted to guide the development of toxicogenomics databases underway at the NIEHS National Center for Toxicogenomics, USA (NCT 2006), and at the EMBL European Bioinformatics Institute, UK (EMBL EBI 2007), in conjunction with the International Life Sciences Institute’s Health and Environmental Sciences Institute, USA (ILSI HESI 2007).

MIAME/Tox is continuously developing in accordance with our understanding of microarray technology and its applications to toxicology and pharmacology. Please join the MIAME/Tox discussion list (mged-tox@lists.sourceforge.net) and contribute with your ideas and comments.

MIAME/TOX CHECKLIST

Minimum information to be recorded about toxicogenomics experiments is defined in subsequent sections and should include the following data domains:

  • Agent description, formulation, purity, solubility, vehicle, separation methods, chemical structure, active moieties, safety and toxicity, storage, half-life.

  • Experimental design parameters, genetic background and animal husbandry information or cell line and culture information, exposure parameters, dosing regimen, and dose groups.

  • Microarray data, specifying the number and details of replicate array bioassays associated with particular samples, and including PCR transcript analysis if available.

  • Biological endpoint data, including animal and organ weights at necropsy or cell counts and doubling times, clinical chemistry and enzyme assays, hematology, urinalysis, other.

  • Textual endpoint information such as clinical and gross observations, pathology and microscopy findings.

As with MIAME, MIAME/Tox has two major sections.

  • Array design description;

  • Gene expression experiment description.

The first section remains identical to the MIAME 1.1 document, and the second section is extended to fulfill the need of this toxicogenomics-specific application of MIAME. The two components of MIAME/Tox are discussed in further detail below.



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