Investigation

1.1.1.1       Description

The ISA-TAB Investigation file allows for the description of the primary investigation and associated studies including assays and protocols.  For example, an investigation title may be “Dendrimer-Based MRI Contrast Agents” and associated studies may be “Characterizing the Size of Dendrimer based MRI Contrast Agents” and “Determining the Hemolytic Properties of Dendrimer based MRI Contrast Agents”. 

The ISA-TAB specification provides flexibility in representing the level of granularity associated with a study; however, the level of granularity should factor in the effective representation of assays and protocols in conformance with the specification.  For example, a study focusing on “Size Characterizations” will have multiple size assay measurements (e.g. Z-Average Size, Hydrodynamic Size) and may involve the use of multiple protocols (e.g. Size by DLS, Size by AFFM).  These can be represented effectively in the ISA-TAB file structure.  A study focusing on “Physico-Chemical Characterizations” would have numerous and diverse assay measurements (e.g. Size, Molecular Weight, Surface, etc.) and protocols and it may be challenging to represent and group the assay measurements and protocols associated with each characterization type.

Studies within the Investigation file provide descriptive information about the study including design descriptors, publications, factors, assays, protocols, and contacts.  This descriptive information lays the foundation for other ISA-TAB files.  For example, the Study Factors section of the Investigation file provides details of the factors (e.g. media solvent, temperature) used in the study.  The value of these factors (e.g. PBS, 25 Celsius) is then specified in the Assay file.

1.1.1.2       File Format

The Investigation file format leverages a vertical based spreadsheet format with columns representing multiple values.  In the example subset of the Investigation file below, column A indicates the field names and columns B and C are field values.

1.1.1.3       nano-TAB Extensions

In support of nano-TAB, the following extensions and constraints were applied to the ISA-TAB Investigation file and are further described in Section 4.

1.1.2       Study file

1.1.2.1       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.

1.1.2.2       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.

1.1.2.3       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: