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ISA-TAB-Nano Standards Re-Use

ISA-TAB TAB

The ISA-TAB-Nano format specification is based on an existing specification developed by the ISA-commmunity (www.isa-tools.org), namely, the investigation/study/assay (ISA-TAB) format specification.  The ISA-TAB format (http://isatab.sourceforge.net/) is used by the ‘omics’ (proteomics, genomics, metabolomics, and transcriptomics) communities to share data and metadata associated with different assays and technology types in their experiments. The ISA-TAB file structure relies on three primary files---investigation, study, and assay (ISA) files. Raw/derived data files and any other files (e.g., image files, protocol documents) specific to each assay are shared along with the three primary ISA-TAB files if the data files are referenced in the primary ISA-TAB files. ISA-TAB does not provide format specification for files other than the investigation, study, and assay files.  The ISA-TAB investigation file is used for three purposes: (1) to record all declarative information referenced in other files; (2) to relate assay files to study files; and (3) to group multiple study files that are part of the same investigation. The ISA-TAB study file is used to record information about the source, sampling methodology, treatment, preparation, and characteristics of the subjects (biospecimens) studied using one or more assays under an investigation.

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

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ISA-TAB-Nano File

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Development

ISA-TAB specifies that the names of the primary files end with .txt extensions.  ISA-TAB-Nano file names may end in either .txt or .xls extensions. 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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In FIG 2, the ISA-TAB-Nano

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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 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 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.

FIG 2. ISA-TAB-Nano File Development Process
diagram of file development process

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.

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.

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