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1.1.1.1       Description

The Assay file describes the protocol parameters and factors (e.g. temperature, media solvent, concentration) associated with each assay and provide references to assay results including measurements, derived data files, and other file types.  There can be multiple Assay files per study.

1.1.1.2       File Format

The ISA-TAB file format leverages a horizontal based spreadsheet format with column headers and row values.  An example subset of this format is provided below.  Please note, concepts specified within the bracket “[]” are variable depending on the type of assay.

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="d45e0f74-4fe9-4506-a851-a9d311b67f9d"><ac:plain-text-body><![CDATA[

Material Sample Name

Assay Name

Factor Value [temperature]

Unit

Measurement Value [size]

Unit

]]></ac:plain-text-body></ac:structured-macro>

NCL-23-F1

Size by DLS

25

Celsius

7.4

nm

NCL-23-F1

Size by DLS

37

Celsius

9.8

nm


1.1.1.3       nano-TAB Extensions

In support of nano-TAB, the following extensions and constraints were applied to the ISA-TAB Assay file and are further described in Section 4.

Field

Change

Description

Field Status

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="0d09c48a-188e-46ef-93a3-36f9af7880ff"><ac:plain-text-body><![CDATA[

Measurement Value[]

Addition

The Measurement Value is leveraged to capture derived data values associated with each assay.  In ISA-TAB this is typically represented in a separate data file; however, in assays in which there are only a few measurements (e.g. Z-Average Size) and it is necessary to display the factors along with the measurements (e.g. temperature), the Measurement Value is leveraged.

]]></ac:plain-text-body></ac:structured-macro>
The NPO provides a list of measurements associated with each assay.

Optional

Statistic

Addition

The ISA-TAB format allows for the specification of units (e.g. mg/mL) but not a statistic (e.g. mean, SD, etc.).

Optional

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="4e86bc05-9036-4cd6-b1f7-71c0a6a0adf6"><ac:plain-text-body><![CDATA[

Factor Value[]

Use NPO

The NPO should be leveraged to obtain a list of valid Factor values which are typically stressors or experimental conditions such as temperature, media solvent, time, and concentration.

Optional

]]></ac:plain-text-body></ac:structured-macro>
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