Biomedical Engineering Reference
In-Depth Information
In combination, these principles require that any solution be simple,
immediately benefi cial, and respectful of existing work. The 'Investigation/
Study/Assay' (ISA) framework, the product of an ongoing collaboration
between various research and service groups actively involved in the
development of community standards [8], offers such a solution. By
providing a generic backbone for structured descriptions of bioscience
research - the Investigation, Study, Assay hierarchy around which all else
is built - the ISA framework simultaneously offers an interim solution
that respects existing data formats and a workable scaffold around which
to build new, integrated standards. The basic ISA backbone, extended in
an appropriately generic manner, has been implemented as 'ISA-Tab' - a
simple format supported by several projects, not least the ISA software
suite whose component modules constitute the core elements of a
collaborative framework [9].
Using the shared, meta-data-focused ISA framework it is now possible
to (1) aggregate investigations of biological systems - where source
material has been subject to several kinds of analyses (e.g. genomic
sequencing, protein-protein interaction assays and the measurement of
metabolite concentrations) - as coherent units of research; (2) perform
meta-analyses; and (3) more straightforwardly submit to public
repositories, where required. The latter, unfortunately, are still designed
for specifi c analyses types, necessitating the fragmentation of data sets
because of the diversity of reporting standards with which the parts must
be formally represented.
7.3 The ISA-Tab format
￿ ￿ ￿ ￿ ￿
ISA-Tab is the result of a painstaking exercise to map a number of
repository submission formats onto one structure for experimental meta-
data, to facilitate bidirectional conversion; leveraging common elements
while intentionally keeping data fi les external in their native or community
formats to side-step interoperability issues. ISA-Tab, illustrated in
Figure 7.1, has become parent to a variety of spreadsheet-based formats
for data sharing [10]. The Investigation fi le contains all the information
needed to understand the overall goals and means used in an experiment;
experimental steps (or sequences of events) are described in the Study and
in the Assay fi le(s). For each Investigation fi le there may be one or more
Study fi le; for each Study fi le there may be one or more Assay fi les.
The Investigation fi le is intended to meet three needs: (1) to defi ne key
entities, such as factors, protocols, parameters, which may be referenced
 
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