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Table of Contents

Scope:

This standard (nano-TAB) specifies the format for representing and sharing information about nanomaterials, small molecules and biological specimens along with their assay characterization data (including metadata, and summary data) using  spreadsheet or TAB-delimited files [1] .

Prerequisites

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

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 [2].  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 [3].  To date, the lack of standardization has been one of the most significant barriers to data sharing. 

1.2 Significance

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.

2. nano-TAB Development  and Use

The nano-TAB project is an effort of the National Cancer Institute (NCI) Cancer Biomedical Informatics Grid (caBIG^®^) Nanotechnology Informatics Working Group (Nano WG).  Its proper use as a standard requires familiarity with other components of the caBIG complement of informatics tools that are all designed to support the meaningful exchange of data across the nanotechnology community.  In Section X, the major components of caBIG are described and adjustments to the existing elements of ISA-TAB are given in Section X.

2.1 nano-TAB format’s relationship to other projects

2.1.1 ISA-TAB 

The nano-TAB format specification is based on an existing specification developed by the European Bioinformatics Institute (EBI), namely, the investigation/study/assay (ISA-TAB) format specification.  The ISA-TAB format 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.

2.1.2 Life Sciences Domain Analysis Model (LS DAM)

The caBIG® (cancer Bioinformatics Grid) LS DAM [6] 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 nanotechnology  subdomain, which was developed based on caNanoLab object model and NPO terms. LS DAM makes a distinction between biospecimens (for example, cell line, tissue samples, body fluid samples, organ parts) and materials that are not derived from a cell, tissue, organ, or body (for example, nanoparticle formulations, drug formulations, solvent, and so forth). This motivated the use of the term “material sample” in the nano-TAB material file.  Weekly Nano WG web-conferencing was used to ensure the alignment of nano-TAB with the LS DAM.   

2.1.3 NanoParticle Ontology (NPO)

Like ISA-TAB, nano-TAB provides fields for entering and referencing terms selected from ontologies and standard terminologies. The ontologies are available at BioPortal (http://www.bioontology.org), which is maintained by the National Center for Biomedical Ontologies.  Though the investigator may use alternative ontology and vocabulary sources, the ability to evaluate and share data require that all parties have access to those being used (they should be available to the investigators). All terms and fields used in this standard utilize the NCI EVS and NanoParticle Ontology elements.

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

2. nano-TAB v0.5 Structure Overview

2.1 nano-TAB Structure

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



Figure 2-1 nano-TAB Structure


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

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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