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Description
The Assay File provides
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, images, raw data files, derived data files, and other file types. There can be multiple Assay files Files per study.
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File Format
unmigratedThe ISA-wiki-markupThe TAB-Nano Assay File leverages 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="74ebe0f5-5821-4939-a068-d4c634ff5ab1"><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.
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Field
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Change
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Description
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Field Status
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<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="f2d967e0-72a4-46fc-a0e3-4505ab090ec0"><ac:plain-text-body><![CDATA[
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Measurement Value[]
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Addition
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Optional
format, which is a horizontal-based spreadsheet format with column headers and row values. The following table provides an example subset of this format. Concepts specified within the bracket “[ ]” are variables depending on the type of assay.
Example Subset of the Assay File Format
A | B | C | E |
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Sample Name | Assay Name | Measurement Value[z-average(hydrodynamic diameter)] | Unit |
NCL-20-1 | size by DLS assay | 5.2 | nm |
NCL-20-2 | size by DLS assay | 8.6 | nm |
Fields
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. In support of ISA-TAB-Nano, extensions were applied to the Assay File to record the endpoint value of an assay measurement (Measurement Value) as an attribute of the assay name.
The Assay File
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Statistic
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Addition
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The ISA-TAB format allows for the specification of units (e.g. mg/mL) but not a statistic (e.g. mean, SD, etc.).
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Optional
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<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="421daeab-af7c-4db3-9d5c-b883b7631ca9"><ac:plain-text-body><![CDATA[
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Factor Value[]
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Use NPO
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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.
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Optional
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]]></ac:plain-text-body></ac:structured-macro>
1.1 Assay file
The Assay file is a horizontally oriented spreadsheet. The file supports the following types of information:s the sample
- Sample name
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- Assay protocol reference
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- , protocol parameter values
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- , performer, and date the
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- protocol was performed
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- Assay factor values including units
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- , if applicable
- Assay name
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- Assay measurement values including units and
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- qualitifed by statistics, if applicable
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- Image files, raw data files, derived data files or
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- other files, if
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- applicable
Nodes
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 with Material Types, The sample name can be a biospecimen, nanomaterial, small molecule, or other material.
Characteristics and/or Comments.
Assay Name---The name of the assay performed. This name is an identifier within the assay file.
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.
D erived Data File---The name or URI of the file resulting from data transformation or processing.
Attributes of Assay Nodes
One or more attributes can be used to provide more information about a assay node. The assay node attributes are described below:
Material Type---An attribute for the Sample Name (for example, 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.
Characteristics [ ]---An attribute for Sample Name if the same attribute is not given in the study file.
Attributes of Processing Events for Assay Nodes
One or more attributes can be used to describe a step in the assay of a sample.
Protocol REF--Assay Protocol Ref - The name of the protocol used to perform the experiment.
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*Parameter Value \[\] --* Values of concepts associated with an experiment protocol that are not varied in the experiment. Parameters concepts are variable and described in brackets. |
Performer - The full name of the individual performing the assay.
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. This name should be obtained from a value for the field study protocol name in the investigation file. Protocol REF can be further described using the following fields:
Parameter Value [ ]--- Value of a parameter, which is an intrinsic experimental condition that may be varied or 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.
Performer---The name of the person who carried out the protocol.
Date---The calendar day on which the
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protocol was carried out. The date format should be in YYYY-MM-DD.
Assay Name - The name of the assay performed.
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*Factor Value \[\] -* An independent variable manipulated by the experimentalist with the intention to affect biological systems (i.e. stressor). Factor concepts are variable and described in brackets. |
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*Measurement Value \[\] -* The endpoint of the assay. Measurement value concepts are variable and described in brackets. |
Unit - The standard of measurement.
Statistic - A datum that can be represented numerically.
Attribute of Assay Name
One or more attributes can be used to record the assay endpoints.
Factor Value [ ]---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. Factor Value [] in the Assay file should reference technical variations (such as software, instrument or protocol variations).
Measurement Value [statistic(measurement name)]---The endpoint of the assay. Measurement value names are described in brackets or parenthesis if a statistics (such as mean, standard deviation) is applied to the measurement (Syntax: Measurement Value[statistic(<measurement name>)]). A statistic is only required for statistical measures.
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 [ ], factor value [ ], or measurement value [ ] columns are quantitative and dimensional. If the term for unit is from an ontology/controlled vocabulary, then its term accession number and the term source REF should be defined in the ISA-TAB-Nano Assay File.
Term Accession Number---Term Accession Number - Identification number of a term selected from an ontology or a controlled vocabulary, and if the term is entered as a value for the Unit.
value in material type, characteristics [ ], parameter value [ ], measurement value [], unit or factor value [ ] columns.
Term Source REF---The name which identifies the source from where Term Source Ref - Name of the ontology or controlled vocabulary from which a term is selected and entered as a value for the Unit.
The Assay file will vary depending on the type of assay performed and protocol and technology type leveraged. Provided below are examples only of Assay files for some of the common types of assays identified across nanotechnology resources.
1.1.1 Example Assay file: Size by Dynamic Light Scattering (DLS)
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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 Assay Fields
Comment [ ]---Any comment that provides additional information, which is added only when no other appropriate field exists. Comment fields should be attached to the closest node or the field.
Files
The following pages provide the assay file examples, template, and glossary:
Exhibit 4.15 Example Assay file for Size by DLS
1.1.2 Example Assay file: Zeta Potential
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Exhibit 4.16 Example Assay file for Zeta Potential
1.1.3 Example Assay file: Assay file for Hemolysis
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Exhibit 4.17 Example Assay file for Hemolysis
1.1.4 Example Assay file: Assay file for Cell Viability (MTT)
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Exhibit 4.18 Example Assay file for Cell Viability (MTT)
1.1.5 Example Assay file: Assay file for Caspase 3 Apoptosis
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Exhibit 4.19 Example Assay file for Caspase Apoptosis
1.1.6 Example Assay file: Assay file for Pharmacokinetics
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