...

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.

...

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^{Image Removed}), 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 NanoParticle Ontology elements.

3.2.1.4.2 NanoParticle Ontology (NPO)--- 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]

1.3 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. 
\\

The NPO is being further developed for the following purposes: 1) to provide terms for annotating data generated from research in nanotechnology, 2) to provide the knowledge framework required for developing data sharing models and standards in nanomedicine, 3) to enable semantic integration of data by providing the terms and relationships for data annotation, 4) to enable unambiguous interpretation of data pertaining to the description and characterization of nanomaterials, and 5) to enable knowledge-based searching of the data for accessing and retrieving relevant information, which in turn facilitates comparison of nanomaterial descriptions and characterization results, leading towards knowledge enhancement and discovery.

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. nano-TAB v0.5 Structure Overview

...