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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 nano-TAB, 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 nano-TAB material file name is referenced as a qualifier for the source sample (nanomaterial) in the study file.
File Format
The nano-TAB 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 1.
TABLE 1: Example Subset of the Study File Format
A | B | C | ||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="33d82384-4d06-4c9a-95d2-4c6b3d749e7d"><ac:plain-text-body><![CDATA[ | Source Name | Material Type | Characteristic[cell type] | ]]></ac:plain-text-body></ac:structured-macro> |
LLC-PK1 | biospecimen | porcine proximal tubule cells | ||
LLC-PK1 | biospecimen | porcine proximal tubule cells |
Fields
Nano-TAB 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.
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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. [TABLES 2 and 3 |ICR:Study File Examples]on the Study Files Examples page provide additional examples of files using these different types of fields |
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Nodes
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_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_. |
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(
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1
...
)
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If
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the
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sample
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assayed
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is
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a
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biological
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specimen,
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its
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source
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is
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the
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starting
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biological
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material
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from
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which
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the
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sample
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was
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derived
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after
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the
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application
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of
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a
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protocol.
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The
...
name
...
of
...
the
...
source
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typically
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refers
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to
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the
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cell
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line
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or
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animal
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number
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for
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biological
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specimens.
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(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 nano-TAB material file.
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_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_. |
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Attributes
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of
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Study
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Nodes
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One
...
or
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more
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attributes
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are
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used
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to
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provide
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more
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information
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about
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a
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study
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node.
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The
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different
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node
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attributes
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are
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described
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below:
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Material
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type
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---An
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attribute
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for
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the
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source
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name
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or
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sample
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name
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(e.g.,
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biospecimen,
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nanoparticle
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sample,
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small
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molecule
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etc.).
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The
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term
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can
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be
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a
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free-text
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description
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or
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taken
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from
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an
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ontology
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or
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a
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controlled
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vocabulary.
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If
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it
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is
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the
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latter,
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then
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the
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following
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qualifiers
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are
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used:
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term
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accession
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number
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and
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term
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source
...
REF
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.
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_Characteristic\[\]_\---An attribute for _source name_ and _sample name_. The term for each characteristic\[\] attribute is written within brackets (e.g., Characteristic \[organism\], Characteristic \[cell type\], etc.). |
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Material
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File
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---The
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name
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of
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the
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nano-TAB
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material
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file
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that
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contains
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detailed
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descriptions
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of
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the
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source
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sample.
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This
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column
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is
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not
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applicable
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for
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biospecimens.
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Provider
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---An
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attribute
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for
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source
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name
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,
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which
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refers
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to
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the
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name
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of
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the
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person
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or
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the
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vendor
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providing
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the
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source
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sample.
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Attributes
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of
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processing
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events
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for
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study
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nodes--
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-
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One
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or
...
more
...
attributes
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are
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used
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to
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describe
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a
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step
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in
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the
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preparation
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of
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a
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sample.
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Protocol
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REF
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---The
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name
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of
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the
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protocol
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used
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to
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prepare
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the
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sample.
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This
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name
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should
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match
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a
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value
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for
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the
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field
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study
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protocol
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name
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in
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the
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investigation
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file
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(within
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the
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study
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protocols
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section).
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Performer
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---The
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name
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of
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the
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person
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who
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carried
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out
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the
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protocol.
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_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 (e.g., 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\[date received\]). |
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_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 nano-TAB investigation file. |
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Qualifiers
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for
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Study
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Nodes’
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Attributes
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Each
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node
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attribute
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may
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be
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qualified
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using
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the
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following
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concepts,
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if
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applicable.
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_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 nano-TAB investigation file. |
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_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. |
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Term
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Source
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REF
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---The
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name
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which
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identifies
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the
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source
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from
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where
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a
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term
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is
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selected
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and
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entered
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in
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nano-TAB
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study
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files.
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This
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name
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should
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match
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one
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of
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the
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names
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entered
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in
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the
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term
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source
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name
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field
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in
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the
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nano-TAB
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investigation
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file.
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Other
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study
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fields
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_Factor Value\[<factor name>\]_\---The value of an independent variable manipulated by the experimentalist with the intention to affect the subject of study (i.e. stressor). Factor terms are given in brackets, and must be defined in the nano-TAB investigation file in the STUDY FACTORS section. |
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_Comment\[\]_\---Any comment that provides additional information, which is added only when no other appropriate field exists. |
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Material
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File
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-
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-
