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The nano-TAB specification is intended to facilitate the submission and exchange of nanomaterial descriptions and characterization data (metadata and summary data) along with the other files (raw/derived data files, image files, protocol documents, etc.) among individual researchers and to/from nanotechnology resources like the NCI’s cancer Nanotechnology Laboratory (caNanoLab) portal \[4[#_ftn1]\] and the Nanomaterial-Biological Interactions (NBI) knowledgebase \[5[|#_ftn2]\].  Nano-TAB also serves to empower organizations to adopt standard methods for representing data in nanotechnology publications; and to provide researchers with guidelines for representing nanomaterials and characterizations to achieve cross-material comparison.

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NanoParticle Ontology (NPO) \[7\] is an ontology that is designed and developed within the framework of the Basic Formal Ontology (BFO) \[8\] and implemented in the ontology web language (OWL) \[9\]. It is being developed to represent the knowledge underlying the description, preparation, and characterization of nanomaterials. NPO development began with the representation of knowledge underlying the chemical composition, preparation, physiochemical, and functional/biological characterization of nanoparticles that are formulated and tested for applications in cancer diagnostics and therapeutics. The NPO provided the knowledge framework for developing the nano-TAB material file format. The NPO provides a subset of the terms and relationships for the description and characterization of nanomaterials in the nano-TAB file format.  The NPO is being further developed for the following purposes: (1) to provide terms for annotating nanotechnology research data; (2) to provide the knowledge framework required for developing data-sharing models and standards in nanomedicine; (3) to enable semantic integration of data; (4) to enable unambiguous interpretation of the description and characterization of nanomaterials; and (5) to enable knowledge-based searching  and comparison of nanomaterial descriptions and characterization results.[\_msoanchor_1|#_msoanchor_1]

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2 Requisite Adjustments to ISA-TAB Practice to be Found in Nano-TAB

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Nano-TAB extension to ISA-TAB--- While

2.1 nano-TAB Structure

nano-TAB leverages and extends the three primary ISA-TAB file structure to capture nanotechnology metadata (Figure 2-1).

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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 (e.g., image files, protocol documents) specific to each assay have to be shared along with the four primary nano-TAB files.  Nano-TAB does not provide any specification for how to format files other than the four primary files:  investigation, study, assay and material files.  Although nano-TAB 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 nano-TAB files.

2.2.1 Distinction between biological and non-biological samples 

In nanotechnology, samples from biological and non-biological sources can be the primary subjects of a study.    Therefore, in nano-TAB, 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 nano-TAB, 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 nano-TAB, the material file is used to describe material samples, while the study file is used to describe biospecimens. 

2.2.2 ISA-TAB and nano-TAB file names

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

3. nano-TAB v0.6 Files and Structure

3.1 nano-TAB File Structure

Nano-TAB 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 nano-TAB files have to be shared along with the nano-TAB files.

When sharing primary nano-TAB 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.    

Nano-TAB File Development Process

 In FIG 2, the nano-TAB 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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Once the nano-TAB files have been created, the files can be validated and submitted into nanotechnology resources that support the nano-TAB 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 \[10\][|#_ftn1].  It is also anticipated that nanotechnology resources like caNanoLab, the Nanomaterial-Biological Interactions (NBI) knowledgebase (http://nbi.oregonstate.edu/), and other resources will provide facilities for importing/exporting nano-TAB files as the nano-TAB specification evolves

The ISA-TAB file structure relies on three primary files - Investigation, Study, and Assay files.  Data files specific to each assay can also be provided to capture assay specific measurements.  nano-TAB leverages and extends ISA-TAB by introducing a Materials file for representing the structural composition of the nanomaterial.  nano-TAB extends the ISA-TAB Study file which traditionally provides a mapping between studies and biological specimens, by referencing the Material file for mapping the study to nanomaterials or small molecules.

Each file has a defined structure and is described throughout this section.  Detailed descriptions of the contents of each file with nanotechnology examples are provided in Section 4 and Appendix A.

2.2 nano-TAB file Development Process

Figure 2-2 describes the nano-TAB file development process.  Typically, the Investigation file is developed first and describes the overall investigation and associated studies.  The Investigation file is a text file with a naming convention of “i_xxx.txt”, where 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”) can be created.  The Study file describes any samples (biospecimens, nanomaterials, small molecules) leveraged in the study.  The Material file describes the nanomaterial (or small molecule) and its components including structural information and follows the naming convention “m_xxx.txt”.  The Material file provides valuable information allowing for cross-particle comparison across nanotechnology resources.  Assay files (following the convention “a_xxx.txt”) are created for all assays performed.  Assay files include associated data files that are specific to the assay type being performed.

Once the nano-TAB files have been created, the files can be validated and submitted into nanotechnology resources that support the nano-TAB 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.  It is also anticipated that nanotechnology resources like caNanoLab, the NBI, and other resources will provide facilities for importing/exporting nano-TAB files as the nano-TAB specification evolves.

3. Relationship to Other Standards

3.1 ISA-TAB

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nano-TAB file format leverages and extends the investigation, study, and assay files of the ISA-TAB (Investigation/Study/Assay-TAB delimited) format.  The ISA-TAB format is a general purpose framework for sharing metadata and data from omics-based experiments \[ref\].  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. The nano-TAB format includes an additional type of file called the Material file which is used to record information about the chemical and structural descriptions of the nanomaterial formulations and other types of chemical samples (e.g., drug formulations). The ISA-TAB Assay file is used to record information about the assay protocols and references to data files.

3.2 NanoParticle Ontology (NPO)

Section 1.3 provides a brief overview of the NanoParticle Ontology (NPO).  The NPO will provide the terms and relationships for the description and characterization of nanomaterials in the nano-TAB file format.  NPO also provides the knowledge framework for developing and using the Material file format.

3.3 LS DAM

The caBIG Life Sciences Domain Analysis Model (LS DAM) provides a shared view of the semantics of the life sciences domains that are represented by the different workspaces in the caBIG infrastructure. It has a nano sub domain, which was developed based on caNanoLab object model and NPO terms. LS DAM makes a distinction between biospecimens (e.g., cell line, tissue samples, body fluid samples, organ parts) and materials that are not derived from a cell, tissue, organ or body (e.g., nanoparticle formulations, drug formulations, solvent, etc.). This motivated the use of the term “material sample” in the nano-TAB material file

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