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Familiarity with the fields of nanotechnology and nanomedicine is a pre-requisite for this specification.  An understanding of ISA-TAB is recommended but not required as the nano-TAB specification provides descriptive information on ISA-TAB as applied to nanotechnology.

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nano-TAB Introduction

1.1 Rationale

Nanobioinformatics has been largely recognized as an essential element of our nation’s competitiveness in nanotechnology and a rational approach to employ weight-of-the-evidence strategies that ensure its safe development according to the National Nanotechnology Initiative, 2006. The ability to manipulate matter at the atomic scale will enable a broad range of beneficial applications in the electronics, healthcare (e.g. nanomedicine, imaging, and diagnostics), cosmetics, technologies and engineering industries.  Pertinent to the development of promising biomedical nanotechnologies and to the safety of nanoscale materials in general, is a thorough understanding of nanomaterial-biological interactions.  However, a rational approach must be employed early on in nanotechnology evolution to direct the safe development of novel nanotechnologies and provide accurate predictions of nanomaterial-biological interactions based on weight-of-the-evidence (Dahl et al., 2007; McKenzie and Hutchison, 2004). This inevitably will require data mining and computer simulation for visualization of the important parameters in an almost infinite set of data from global research efforts in nanoscience and nanotechnology (Teeguarden et al., 2007).  To date, the lack of standardization has been one of the most significant barriers to data sharing. 

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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.

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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.

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3 Relationship to Other Standards

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ISA-TAB

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.

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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.

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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.