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ISA-TAB-Nano Extensions to ISA-TAB

ISA-TAB-Nano extension to ISA-TAB--- While ISA-TAB-Nano leverages the three primary ISA-TAB files, it extends ISA-TAB by providing specification for a fourth file (called the material file) for representing the composition and characteristics of nanoparticle formulations and small molecules. Raw/derived data files and any other files (for example, image files, protocol documents) specific to each assay have to be shared along with the four primary ISA-TAB-Nano files. ISA-TAB-Nano does not provide any specification for how to format files other than the four primary files: investigation, study, assay and material files. Although ISA-TAB-Nano adopts ISA-TAB field names and their definition in the investigation, study, and assay files, some of the definitions are modified and additional fields are introduced. These modifications and extensions are required to expand the scope of information captured from nanotechnology data sets into the ISA-TAB-Nano files.

Distinction between

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Biological and

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Non-biological

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Samples

In nanotechnology, samples from biological and non-biological sources can be the primary subjects of a study. Therefore, in ISA-TAB-Nano, samples derived from biological sources are called biological specimens or biospecimens (for example, cell line, body fluids, organs, etc.). Whereas, samples derived from non-biological sources are simply called material samples (for example, nanomaterials, nanoparticle formulations, small molecules). 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). Hence, in ISA-TAB-Nano, the concept of a sample (as used in ISA-TAB specification) is redefined to include both biological specimens and material samples. The ISA-TAB study file can only be used to record the source and characteristics of biospecimens studied in an assay, and cannot support the representation of materials. Therefore, in ISA-TAB-Nano, the material file is used to describe material samples, while the study file is used to describe biospecimens.

Extensions to ISA-TAB Files

The Table below represents extensions made to each ISA-TAB file in support of ISA-TAB-Nano.

ISA-TAB Extension Field Name

ISA-TAB File

Purpose

Investigation Disease

Investigation

To capture and retrieve investigations associated with specific disease modalities such as cancer

Investigation Disease Term Accession Number

Investigation

To enable semantic interoperability for disease terms

Investigation Disease Term Source REF

Investigation

To enable semantic interoperability for disease terms

Investigation Outcome

Investigation

To enable researchers to review the outcomes of investigations for assessing the utility of the investigation in achieving scientific endpoints

Study Disease

Investigation

To capture and retrieve studies associated with specific disease modalities such as cancer

Study Disease Term Accession Number

Investigation

To enable semantic interoperability for disease terms

Study Disease Term Source REF

Investigation

To enable semantic interoperability for disease terms

Study Outcome

Investigation

To enable researchers to review the outcomes of studies for assessing the utility of the investigation in achieving scientific endpoints

Study Factor Name Term Accession Number

Investigation

To enable semantic interoperability for study factor name

Study Factor Name Term Source REF

Investigation

To enable semantic interoperability for study factor names

Study Assay Measurement Name

Investigation

To capture the variables measured in an assay to support cross study analysis

Study Assay Measurement Name Term Accession Number

Investigation

To enable semantic interoperability for assay measurement names

Study Assay Measurement Name Term Source REF

Investigation

To enable semantic interoperability for assay measurement names

Material Source Name

Study, Material

To provide a reference for the material associated with the study

Material File

Study

To provide a reference for the ISA-TAB-Nano material file that describes the material samples of a study

Measurement Value

Assay

To record the endpoint value of an assay measurement within the assay file

Statistic

Assay

To capture the statistical measures (e.g. mean, SD) associated with a measurement or factor value

All Fields

Material

To describe nanomaterials and small molecules

 

ISA-TAB-Nano File Structure

ISA-TAB-Nano uses the three primary files of ISA-TAB-- investigation file, study file, and assay file; and, introduces a fourth file called the material file (FIG 1). Other files such as raw/derived data files, image files, protocol documents, etc., referenced in the ISA-TAB-Nano files have to be shared along with the ISA-TAB-Nano files.

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