The study file provides a mapping between the samples (biospecimens and material samples) and processing events (occurs whenever a protocol is applied) associated with a study. It is also used to provide values for the parameters and factors associated with an assay of the sample. In nano-TAB, factors can be either entered in the study file or in the assay file. 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, and so forth). The nanomaterial applied to a biospecimen in an in vitro or in vivo assay is considered as a study factor along with other factors that vary in the experiment (for example, dose). The study file is required as it functions as the primary mapping file between the samples and the assay. For studies involving nanomaterials (also applies to small molecules), the material file allows for a detailed description of the composition and characteristics of the nanomaterial, and the nano-TAB material file name is referenced as a qualifier for the source sample (nanomaterial) in the study file.
The nano-TAB study file leverages the ISA-TAB file format, which is a horizontal-based spreadsheet format with column headers in the first row. An example subset of this format is provided in TABLE 3. Please note, the concept specified within the bracket “[ ]” is a variable depending on the type of sample.
Nano-TAB extends the ISA-TAB specification for the study file by redefining the concept of a sample and adding a new field called material file to reference the material files that contain description of the material samples.