Study

1.1.1.1       Description

The Study file provides a mapping between the samples, materials, and processing events associated with a study.  Samples can be biological materials (e.g. cell line, animal), nanomaterials, or small molecules.  For physico-chemical characterizations of nanomaterials, the sample is the nanomaterial.  For in vitro and in vivo characterizations, the sample is the biological specimen (cell line, animal, etc.).  The nanomaterial applied to the sample is considered a Study Factor along with other factors that vary in the experiment (e.g. dose).  The Study file is required as it functions as the primary mapping between the samples and the study.  For studies involving nanomaterials, the Material file is references as a qualifier and allows for a detailed description of the composition and characteristics of the nanomaterial.

1.1.1.2       File Format

The ISA-TAB file format leverages a horizontal based spreadsheet format with column headers and row values.  An example subset of this format is provided below.  Please note, concepts specified within the bracket “[]” are variable depending on the type of sample.

1.1.1.3       nano-TAB Extensions

In nanotechnology, both the material and specimen can function as the primary subject of the study and as such, nano-TAB re-defined the concept of a sample to include both biological specimens and materials.  To accommodate additional metadata needed to effectively describe the material sample, a Material file was introduced.

To accommodate the nano-TAB changes, references to the sample were renamed and are identified as follows: