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Description
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 ISA-TAB-Nano,
...
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
...
ISA-TAB-Nano
...
material
...
file
...
name
...
is
...
referenced
...
as
...
a
...
qualifier
...
for
...
the
...
source
...
sample
...
(nanomaterial)
...
in
...
the
...
study
...
file.
...
File
...
Format
...
The
...
ISA-TAB-Nano
...
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
...
14.
...
TABLE
...
14:
...
Example
...
Subset
...
of
...
the
...
Study
...
File
...
Format
...
A | B | C |
|---|---|---|
Source Name | Material Type | Characteristic[cell type] |
LLC-PK1 | biospecimen | porcine proximal tubule cells |
LLC-PK1 | biospecimen | porcine proximal tubule cells |
Fields
ISA-TAB-Nano
...
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.
...
Please
...
note,
...
the
...
concept
...
specified
...
within
...
the
...
bracket
...
“
...
[
...
]”
...
is
...
a
...
variable
...
depending
...
on
...
the
...
type
...
of
...
sample.
...
According
...
to
...
the
...
ISA-TAB
...
specification,
...
the
...
Study
...
file
...
has
...
different
...
types
...
of
...
fields
...
called
...
nodes,
...
attributes
...
of
...
nodes,
...
qualifiers
...
of
...
nodes’
...
attributes,
...
and
...
other
...
valid
...
fields.
...
...
...
...
...
on
...
the
...
Study
...
Files
...
Examples
...
page
...
provide
...
additional
...
examples
...
of
...
files
...
using
...
these
...
different
...
types
...
of
...
fields.
...
Nodes
Source Name---The
...
unique
...
identification
...
name
...
of
...
the
...
source
...
from
...
where
...
the
...
sample
...
is
...
derived.
...
Source
...
names
...
can
...
be
...
qualified
...
using
...
the
...
following
...
column
...
attributes:
...
characteristic
...
[
...
],
...
material
...
type
...
,
...
material
...
file
...
,
...
provider
...
,
...
and
...
comment
...
.
...
(
...
1
...
)
...
If
...
the
...
sample
...
assayed
...
is
...
a
...
biological
...
specimen,
...
its
...
source
...
is
...
the
...
starting
...
biological
...
material
...
from
...
which
...
the
...
sample
...
was
...
derived
...
after
...
the
...
application
...
of
...
a
...
protocol.
...
The
...
name
...
of
...
the
...
source
...
typically
...
refers
...
to
...
the
...
cell
...
line
...
or
...
animal
...
number
...
for
...
biological
...
specimens.
...
(
...
2
...
)
...
If
...
the
...
sample
...
assayed
...
is
...
a
...
material
...
that
...
is
...
not
...
derived
...
from
...
a
...
biological
...
source,
...
then
...
the
...
corresponding
...
source
...
name
...
should
...
refer
...
to
...
the
...
starting
...
sample
...
that
...
was
...
modified
...
by
...
a
...
protocol
...
for
...
the
...
assay.
...
In
...
this
...
case,
...
the
...
source
...
name
...
should
...
match
...
the
...
value
...
recorded
...
for
...
material
...
source
...
identifier
...
in
...
the
...
corresponding
...
ISA-TAB-Nano
...
material
...
file.
...
Sample
...
Name
...
---The
...
unique
...
identification
...
name
...
of
...
the
...
sample.
...
The
...
sample
...
is
...
obtained
...
after
...
the
...
application
...
of
...
a
...
protocol
...
Sample
...
names
...
can
...
be
...
qualified
...
using
...
the
...
following
...
column
...
attributes:
...
characteristic
...
[
...
],
...
material
...
type
...
,
...
material
...
file
...
,
...
and
...
comment
...
.
...
Attributes
...
of
...
Study
...
Nodes
...
One
...
or
...
more
...
attributes
...
are
...
used
...
to
...
provide
...
more
...
information
...
about
...
a
...
study
...
node.
...
The
...
different
...
node
...
attributes
...
are
...
described
...
below:
...
Material
...
type
...
---An
...
attribute
...
for
...
the
...
source
...
name
...
or
...
sample
...
name
...
(for
...
example,
...
biospecimen,
...
nanoparticle
...
sample,
...
small
...
molecule
...
etc.).
...
The
...
term
...
can
...
be
...
a
...
free-text
...
description
...
or
...
taken
...
from
...
an
...
ontology
...
or
...
a
...
controlled
...
vocabulary.
...
If
...
it
...
is
...
the
...
latter,
...
then
...
the
...
following
...
qualifiers
...
are
...
used:
...
term
...
accession
...
number
...
and
...
term
...
source
...
REF
...
.
...
Characteristic
...
[
...
]
...
---An
...
attribute
...
for
...
source
...
name
...
and
...
sample
...
name
...
.
...
The
...
term
...
for
...
each
...
characteristic
...
[
...
]
...
attribute
...
is
...
written
...
within
...
brackets
...
(for
...
example,
...
Characteristic
...
[organism
...
],
...
Characteristic
...
[cell
...
type
...
],
...
etc.).
...
Material
...
File
...
---The
...
name
...
of
...
the
...
ISA-TAB-Nano
...
material
...
file
...
that
...
contains
...
detailed
...
descriptions
...
of
...
the
...
source
...
sample.
...
This
...
column
...
is
...
not
...
applicable
...
for
...
biospecimens.
...
Provider
...
---An
...
attribute
...
for
...
source
...
name
...
,
...
which
...
refers
...
to
...
the
...
name
...
of
...
the
...
person
...
or
...
the
...
vendor
...
providing
...
the
...
source
...
sample.
...
Attributes
...
of
...
processing
...
events
...
for
...
study
...
nodes--
...
-
...
One
...
or
...
more
...
attributes
...
are
...
used
...
to
...
describe
...
a
...
step
...
in
...
the
...
preparation
...
of
...
a
...
sample.
...
Protocol
...
REF
...
---The
...
name
...
of
...
the
...
protocol
...
used
...
to
...
prepare
...
the
...
sample.
...
This
...
name
...
should
...
match
...
a
...
value
...
for
...
the
...
field
...
study
...
protocol
...
name
...
in
...
the
...
investigation
...
file
...
(within
...
the
...
study
...
protocols
...
section).
...
Performer
...
---The
...
name
...
of
...
the
...
person
...
who
...
carried
...
out
...
the
...
protocol.
...
Date
...
---The
...
calendar
...
day
...
on
...
which
...
the
...
protocol
...
was
...
carried
...
out.
...
The
...
date
...
format
...
should
...
be
...
in
...
YYYY-MM-DD.
...
If
...
there
...
are
...
other
...
dates
...
to
...
be
...
recorded
...
(for
...
example,
...
the
...
date
...
when
...
a
...
sample
...
was
...
received
...
from
...
a
...
vendor),
...
one
...
should
...
create
...
a
...
comment
...
[
...
]
...
column
...
and
...
specify
...
the
...
type
...
of
...
date
...
within
...
the
...
square
...
brackets
...
(e.g.,
...
Comment
...
[date
...
received
...
]).
...
Parameter
...
value
...
[<parameter
...
term
...
]
...
---Value
...
of
...
a
...
parameter,
...
which
...
is
...
kept
...
constant,
...
when
...
applying
...
a
...
protocol.
...
The
...
parameter
...
term
...
is
...
written
...
within
...
brackets
...
and
...
must
...
match
...
the
...
term
...
used
...
as
...
value
...
for
...
the
...
study
...
protocol
...
parameter
...
name
...
in
...
the
...
ISA-TAB-Nano
...
investigation
...
file.
...
Qualifiers
...
for
...
Study
...
Nodes’
...
Attributes
...
Each
...
node
...
attribute
...
may
...
be
...
qualified
...
using
...
the
...
following
...
concepts,
...
if
...
applicable.
...
Unit
...
---The
...
standard
...
of
...
measurement
...
used
...
if
...
the
...
values
...
for
...
characteristic
...
[
...
],
...
parameter
...
value
...
[
...
]
...
or
...
factor
...
value
...
[
...
]
...
columns
...
are
...
quantitative
...
and
...
dimensional.
...
If
...
the
...
term
...
for
...
unit
...
is
...
taken
...
from
...
an
...
ontology/controlled
...
vocabulary,
...
then
...
its
...
term
...
accession
...
number
...
and
...
the
...
term
...
source
...
REF
...
should
...
be
...
defined
...
in
...
the
...
ISA-TAB-Nano
...
investigation
...
file.
...
Term
...
Accession
...
Number
...
---Identification
...
number
...
of
...
a
...
term
...
selected
...
from
...
an
...
ontology
...
or
...
a
...
controlled
...
vocabulary,
...
if
...
the
...
term
...
is
...
entered
...
as
...
a
...
value
...
in
...
source
...
name
...
,
...
material
...
type,
...
characteristic
...
[
...
]
...
,
...
parameter
...
value
...
[
...
]
...
,
...
unit
...
or
...
factor
...
value
...
[
...
]
...
columns.
...
Term
...
Source
...
REF
...
---The
...
name
...
which
...
identifies
...
the
...
source
...
from
...
where
...
a
...
term
...
is
...
selected
...
and
...
entered
...
in
...
ISA-TAB-Nano
...
study
...
files.
...
This
...
name
...
should
...
match
...
one
...
of
...
the
...
names
...
entered
...
in
...
the
...
term
...
source
...
name
...
field
...
in
...
the
...
ISA-TAB-Nano
...
Investigation
...
file.
...
Other
...
study
...
fields
...
Factor
...
Value
...
[<factor
...
name>
...
]
...
---The
...
value
...
of
...
an
...
independent
...
variable
...
manipulated
...
by
...
the
...
experimentalist
...
with
...
the
...
intention
...
to
...
affect
...
the
...
subject
...
of
...
study
...
(that
...
is,
...
stressor).
...
Factor
...
terms
...
are
...
given
...
in
...
brackets,
...
and
...
must
...
be
...
defined
...
in
...
the
...
ISA-TAB-Nano
...
investigation
...
file
...
in
...
the
...
STUDY
...
FACTORS
...
section.
...
Comment
...
[
...
]
...
---Any
...
comment
...
that
...
provides
...
additional
...
information,
...
which
...
is
...
added
...
only
...
when
...
no
...
other
...
appropriate
...
field
...
exists.
