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The study file provides a mapping between the samples (biospecimens and material samples) and processing events (occurs whenever a protocol is applied) associated with a study. It is also used to provide provides values for the parameters and factors associated with an assay of the sample. In ISA-TAB-Nano, factors can be either entered in the study file or in the assay file. For physico-chemical characterizations of nanomaterials, the sample is the nanomaterial. For in-vitro and in-vivo characterizations, the sample is the biological specimen (cell line, animal, and so forth). The nanomaterial applied to a biospecimen in an in-vitro or in-vivo assay is considered as a study factor along with other factors that vary in the experiment (for example, dose). The study file is required as it functions as the primary mapping file between the samples and the assay. For studies involving nanomaterials (also applies to small molecules), the material file allows for a detailed description of the composition and characteristics of the nanomaterial, and the ISA-TAB-Nano material file name is referenced as a qualifier for the source sample (nanomaterial) in the study file.
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The ISA-TAB-Nano study file leverages the ISA-TAB file format, which is a horizontal-based spreadsheet format with column headers in the first row. An The following table provides an example subset of this format is provided in TABLE 1.
TABLE 1: Example Subset of the Study File Format
A | B | C |
|---|---|---|
Source Name | Material Type | Characteristic[cell type] |
LLC-PK1 | biospecimen | porcine proximal tubule cells |
LLC-PK1 | biospecimen | porcine proximal tubule cells |
Fields
Please note, the The concept specified within the bracket “[ ]” is a variable depending on the type of sample. According to the ISA-TAB specification, the Study file has different types of fields called nodes, attributes of nodes, qualifiers of nodes’ attributes, and other valid fields. TABLES 15 and 16 on the Study Files Examples The tables on the Study File Example page provide additional examples of files using these different types of fields.
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Attributes of Study Nodes
One or more attributes are can be used to provide more information about a study node. The different node attributes are described below:
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Attributes of processing events for study nodes--- One or more attributes are can be used to describe a step in the preparation of a sample.
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Date---The calendar day on which the protocol was carried out. The date format should be in YYYY-MM-DD. If there are other dates to be recorded (for example, the date when a sample was received from a vendor), one should create a Comment [ ] column and specify the type of date within the square brackets (e.g., such as Comment [date received]).
Parameter Value [<parameter name]---Value of a parameter, which is kept constantmay be invariant, when applying a protocol. The parameter name is written within brackets and must match the term used as value for the Study Protocol Parameter Name in the ISA-TAB-Nano investigation file.
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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 Study File.
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Factor Value [<factor name>]---The value of an experimental variable manipulated by the investigator with the intention to affect the subject of study (e.g. such as stressor). Factor names are given in brackets, and must be defined in the ISA-TAB-Nano investigation file in the STUDY FACTORS section.
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 closest field.
Files
The Study File Examples, Template, and Glossary are provided below.following pages provide the study file examples, template, and glossary:
