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NanoParticle Ontology (NPO) \[[http://www.nano-ontology.org]\] is an ontology that is designed and developed within the framework of the Basic Formal Ontology (BFO) \[2\] and implemented in the ontology web language (OWL) \[3\]. 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 ISA-TAB-Nano material file format. The NPO provides a subset of the terms and relationships for the description and characterization of nanomaterials in the ISA-TAB-Nano 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.