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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 (e.g., cell line, body fluids, organs, etc.).  Whereas, samples derived from non-biological sources are simply called material samples (e.g., 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. 

ISA-TAB

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-Nano

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File Structure

ISA-TAB specifies that the names of the primary files end with .txt extensions.  -Nano uses the three primary files of ISA-TAB-Nano file names may end in either .txt or .xls extensions. The - 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 used as examples in this document were prepared in excel spreadsheets, and so their filenames have the .xls extension.

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have to be shared along with the ISA-TAB-Nano files

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FIG 1. ISA-TAB-Nano File Structure
diagram of file structureImage Added

ISA-TAB and ISA-TAB-Nano File Names

ISA-TAB specifies that the names of files, other files referenced in these files have to be shared along with the primary files end with .  It is anticipated that content management systems will become available to facilitate the sharing and exchange of files.  Until then, these files could be bundled together in a folder and shared as a zip file.txt extensions.  ISA-TAB-Nano file names may end in either .txt or .xls extensions. The ISA-TAB-Nano

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files used as examples in this document were prepared in excel spreadsheets, and so their filenames have the .xls extension.

Sharing ISA-TAB-Nano Files

When sharing primary ISA-TAB-Nano files, other files referenced in these files have to be shared along with the primary files.  It is anticipated that content management systems will become available to facilitate the sharing and exchange of files.  Until then, these files could be bundled together in a folder and shared as a zip file.

ISA-TAB-Nano

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.

FIG 1. ISA-TAB-Nano Structure
diagram of structureImage Removed

ISA-TAB-Nano Files

ISA-TAB-Nano File Development

In FIG 2, the ISA-TAB-Nano file development process is described.  Typically, the investigation file is developed first and describes the overall investigation, associated studies and assays.  The investigation file is a text file with a naming convention of “i_xxx.txt” or “i_xxx.xls,” in which xxx can be any name provided by the investigator.  Once the investigation file has been completed, one or more study files (following the convention “s_xxx.txt” or “s_xxx.xls”) can be created. Similarly, one or more material files can be created.  The material file describes the nanomaterial (or small molecule) and its components including structural information and follows the naming convention “m_xxx.txt” or “m_xxx.xls”.  Assay files (following the convention “a_xxx.txt” or “a_xxx.xls”) are created for all assays performed.  Each assay is defined by the endpoint measured and the technique used to measure that endpoint.  Data files (raw or derived) specific to each type of assay can be associated to the respective assay files by referencing the names of the data files in the assay files.

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Wiki Markup
Once the ISA-TAB-Nano files have been created, the files can be validated and submitted into nanotechnology resources that support the ISA-TAB-Nano specification.  It is anticipated that validation of the files may occur via a validation service that leverages a modified version of the ISA-TAB validator \[[http://isatab.sourceforge.net/validator.html]\].  It is also anticipated that nanotechnology resources like caNanoLab ([https://cananolab.nci.nih.gov/caNanoLab/]), the Nanomaterial-Biological Interactions (NBI) knowledgebase ([http://nbi.oregonstate.edu/]), and other resources will provide facilities for importing/exporting ISA-TAB-Nano files as the ISA-TAB-Nano specification evolves.

ISA-TAB-Nano Files

ISA-TAB-Nano Example Files

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ISA-TAB-Nano XML

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Files

The ISA-TAB-Nano XML specification has been derived from the ISA-TAB-Nano object model.

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