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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 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.

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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.  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.

1        Relationship to Other Standards

1.1       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.

1.2       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.

1.3       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.