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Description

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

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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 The following table provides an example subset of this format is provided in TABLE 1. Please note, concepts . Concepts specified within the bracket “[ ]” are variables depending on the type of assay.

TABLE 1: Example Subset of the Assay File Format

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) and to capture the statistical measures (Statistic) associated with a measurement or factor valueas an attribute of the assay name.

The Assay File supports the following types of information:

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

Nodes

Source Sample Name--- The unique identification name of the source sample, which is referred to from within the study file. This column is used only if the source is the same as the sample in an assay. Source names can be qualified only using Comment.The sample is obtained after the application of a protocol. Sample names can be qualified with Material Types, Characteristics and/or Comments.

Assay 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 Commentassay performed. This name is an identifier within the assay file.

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

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D erived Data File---The name or URI of the file resulting from data transformation or processing.

Attributes of Assay Nodes

assay nodes---One or more attributes are can be 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 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.

Characteristic Characteristics [ ]---An attribute for sample name 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 can be 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. 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 protocol was carried out. The date format should be in YYYY-MM-DD.

Attribute of Assay Name

One or more attributes can be used to record the assay endpoints.

Factor Parameter Value [ ]--- 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 fileThe 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. This field is used to capture measurement outputs recorded in summary dataMeasurement 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

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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 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.

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

Assay 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 characteristics [ ], parameter value [ ], factor measurement value [], measurement unit or factor value [ ], unit, or statistic columns 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 fileInvestigation File.

Other Assay Fields

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).

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:

• Assay File Examples
• Assay File Template
• Assay File Glossary