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Description

The assay file provides references to assay results including measurements, raw data files, derived data files, image files, and other file types.  There can be multiple assay files per study.

File Format

The ISA-TAB-Nano assay file leverages the ISA-TAB file format, which is a horizontal-based spreadsheet format with column headers and row values.  An example subset of this format is provided in TABLE 21.  Please note, concepts specified within the bracket “[ ]” are variables depending on the type of assay.

TABLE 21: Example Subset of the Assay File Format

A

B

C

D

E

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="d0d4756a-f24e-40c6-b598-ddd0d87f6ea2"><ac:plain-text-body><![CDATA[

Sample Name

Assay Name

Measurement Value[hydrodynamic diameter]

Statistic

Unit

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

NCL-20-Sample1

size by DLS assay

5.2

z-average

nm

NCL-20-Sample2

size by DLS assay

8.6

z-average

nm

Fields

ISA-TAB-Nano Extensions---In support of ISA-TAB-Nano, the extensions and constraints in TABLE 2 were applied to the ISA-TAB assay file.  One important extension is that  ISA-TAB-Nano allows the entry of summary data in the assay files through an optional field called Measurement Value.

The assay file is a horizontally oriented spreadsheet, where the field names are organized as column headers in the first row. TABLE 22 - TABLE 25, and TABLE 26 show two examples of an assay file.

According to the ISA-TAB specification, the assay file has different types of fields called nodes, attributes of nodes, qualifiers of nodes’ attributes, and other valid fields. The assay file supports the following types of information:

  •  Source or sample name
  • Assay protocol reference and protocol parameter values
  • Assay name, performer, and date the assay was performed
  • Assay factor values including units and statistics, if applicable
  • Assay measurement values including units and statistics, if applicable
  • Raw data files, derived data files or image files, if applicable

Nodes

Source Name---The unique identification name of the source referred to from within the study file.  This column is used only if the source is same as the sample in an assay. Source names can be qualified only using Comment.

Sample Name--- The unique identification name of the sample, which is referred to from within the study file.  The sample is obtained after the application of a protocol.  Sample names can be qualified only using Comment.

Image file---The name or URI of an image file generated from an assay.

Raw data file---The name or URI of the raw data files.

Derived data file---The name or URI of the file resulting from data transformation or processing.

Attributes of assay nodes---One or more attributes are used to provide more information about a assay node. The different assay node attributes are described below:

Material type---An attribute for the sample name (e.g., biospecimen, nanoparticle sample, small molecule etc.) if the same attribute is not given in the study file.  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 sample name if the same attribute is not given in the study file.

Assay name---The name of the assay performed. This name is used as an identifier within the assay file.

Attributes of Processing Events for Assay Nodes

One or more attributes are used to describe a step in the assay of a sample.

Protocol REF--- The name of the protocol used to perform the experiment. This name should be obtained from a value for the field study protocol name in the investigation file.

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. 

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 investigation file.

Measurement value [<measurement term>]---The endpoint of the assay.  This field is used to capture measurement outputs recorded in summary data.

Qualifiers for Assay 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.

Statistic---The type of statistical measure attributed to a numerical value (e.g., mean, standard deviation, z-average, etc.). This is a required field, if the parameter value, factor value, or measurement value is a statistical measure.

Other Assay Fields

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 ISA-TAB-Nano investigation file in the STUDY FACTORS section.  Factor Value[] in assay file should reference technical variations (such as software, instrument or protocol variations).

Comment[]---Any comment that provides additional information, which is added only when no other appropriate field exists.

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