The Study nodes are denoting the study subjects (biological samples) and the Assay Nodes describe the experiment itself. The samples processing might be more complex than a single step. There could be multiple protocols involved. These could describe biological sample handling, but also data processing.
A study may contain one or more assays. An assay is defined by the endpoint measured (i.e. gene expression) and the technology employed (i.e. DNA microarray). This is described in the Investigation file. The ISA-TAB assay file contains metadata only. The data itself is in external files, which are referred from the Assay file.
To collect investigation data in a consistent manner across the cluster, the ToxBank consortium selected to use ISAcreator, an open access tool (http://isatab.sourceforge.net/isahelp/ch03.html). ISAcreator provides a graphical user interface to create a consistently recorded series of data files that include the ...