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.