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Description
The assay Assay file provides references to assay results including measurements, raw data files, derived data files, image files, and other file types. here There can be multiple assay Assay files per study.
File Format
The ISA-TAB-Nano assay 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 1. Please note, concepts specified within the bracket “[ ]” are variables depending on the type of assay.
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A | B | C | D | E |
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Sample Name | Assay Name | Measurement Value[hydrodynamic diameter] | Statistic | Unit |
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.
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According to the ISA-TAB specification, the assay 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 value.
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 applicableapplicable
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 the same as the sample in an assay. Source names can be qualified only using Comment.
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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 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.
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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.
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Unit---The standard of measurement used if the values for characteristic [ ], parameter value [ ] or factor ,factor value [ ], or measurement value [ ] columns 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.
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 [ ], measurement value [] columns, unit, or statistic 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 (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.
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 (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 assay the Assay file should reference technical variations (such as software, instrument or protocol variations).
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