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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.

1. nano-TAB Introduction

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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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The nano-TAB effort is collaboration between a variety of organizations including the NCI, Washington University, Oregon State University, ONAMI, NIOSH, Stanford University, and ISA-TAB.  nano-TAB is registered as an ASTM Work Item (ASTM WK28974), which facilitates broad community outreach and input to the development of nano-TAB and other standards needed to support nanomedicine.

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2 nano-TAB Development Process

nano-TAB is based on existing standards developed by the European Bioinformatics Institute (EBI) and the Investigation/Study/Assay (ISA-TAB) file format, which represents a variety of assays and technology types.  The nano-TAB specification leverages ISA-TAB files for describing investigations, studies, and assays and provides extensions to support nanomaterial chemical and structural information and assay measurements.  The development of nano-TAB is being facilitated through the use of knowledge that is represented in the NanoParticle Ontology (NPO).

The development of nano-TAB extensions is a community driven initiative established under the caBIG® Nano Working Group (WG).  Nano WG team members met on a weekly basis during the initial development of nano-TAB extensions and will continue to meet on a scheduled basis once nano-TAB extensions have been formalized with the community.  nano-TAB is a registered ASTM Work Item (ASTM WK28974) and it is expected that community feedback will be received through the caBIG Nano WG, pilot efforts with the NCI Cancer Centers of Nanotechnology Excellence (CCNEs), and the ASTM nanotechnology community.

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3 NanoParticle Ontology

The NanoParticle Ontology (NPO) is an ontology that is designed and developed within the framework of the Basic Formal Ontology (BFO) and implemented in the Ontology Web Language (OWL) \[Thomas et al, JBI 2010;  \[http://www.nano-ontology.org\]\]. 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. 
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The NanoParticle Ontology was primarily developed by Dennis Thomas in collaboration with Nathan Baker and Rohit Pappu.  The NPO development was supported by the NIH through grants U54 CA119342 and U54 HG004028.

2        2 nano-TAB v0.5 Structure Overview

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1 nano-TAB Structure

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

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