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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
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