Table 2.

Categories of physicochemical information which the NanoPUZZLES ISA-TAB-Nano templates were designed to capture.

category	template(s)	comments
chemical composition (including surface composition, purity and levels of impurities)	“m_MaterialSourceName.xls”	Only chemical composition information associated with the original / vendor supplied nanomaterial should be reported here, i.e., not adsorption data (see below).
crystal structure/ crystallinity	“m_MaterialSourceName.xls”; “a_InvID_PC_crystallinity_Method.xls”	—
shape	“m_MaterialSourceName.xls”; “a_InvID_PC_shape_Method.xls”	Both qualitative descriptions of shape or “aspect ratio” data [60] can be recorded.
particle size/ size distribution	“m_MaterialSourceName.xls”; “a_InvID_PC_size_Method.xls”; “a_InvID_PC_size_DLS.xls”; “a_InvID_PC_size_TEM.xls”	Dynamic light scattering (DLS) [41] or transmission electron microscopy (TEM) [65–66] measurements are captured using the indicated Assay file templates. Otherwise, unless size values are nominal/vendor supplied, size measurements are captured via the generic Assay file template.
surface area	“m_MaterialSourceName.xls”; “a_InvID_PC_surface area_Method.xls”	This was designed to record “specific surface area” values, i.e., surface area per unit mass [58].
surface charge/ zeta potential	“m_MaterialSourceName.xls”; “a_InvID_PC_zetapotential_Method.xls”	Zeta potential is commonly used as a proxy for surface charge [58].
adsorption	“a_InvID_PC_adsorption_Method.xls”	This was designed to record “adsorption constants” [57] and (equilibrium) adsorption percentages [67] for specific small molecule / macromolecular “probe” species.
reactivity	“a_InvID_PC_reactivity.rateofchange_of.X_SeparationTechnique_Method.xls”	The design of this template reflects the fact that, for some reactivity assays, the analysed species needs to be removed prior to making measurements [68].
dissolution	(1) “a_InvID_PC_dissolution.conc_of.X_SeparationTechnique_Method.xls” ; (2) “a_InvID_PC_dissolution.fraction-dissolved_SeparationTechnique_Method.xls”; (3) “a_InvID_PC_dissolution.rate_of.X_SeparationTechnique_Method.xls”	The design of these templates reflects the fact that a number of different kinds of dissolution measurement may be made for inorganic nanoparticles: (1) the (time dependent) concentrations of various species released by dissolution [67,69] (which may be a redox process [69]); (2) the (time dependent) percentage of original nanoparticles dissolved [70]; (3) the (time dependent) dissolution rate [71]. The design of these templates further reflects the fact that dissolution assay protocols typically employ a separation step to isolate the analysed species [61].
molecular solubility	“a_InvID_PC_solubility_Method.xls”	In the current context, the Chemical Methods Ontology definition of “solubility” [72] was used: “the concentration of a solute in a saturated solution”. This Assay template was specifically designed for recording molecular “solubility” measurements, e.g., the solubility of fullerene nanoparticles [73].
agglomeration/ aggregation	“a_InvID_PC_AAN_BETapproach.xls”	This template was designed for recording the “average agglomeration number” derived from BET gas adsorption data, size measurements and particle density values [58,74]. However, it should be noted that recording of size information obtained under different experimental conditions (using the Assay file templates noted above) may also convey information about the agglomeration state [58]. In addition, a number of physicochemical Assay files (e.g. “a_InvID_PC_size_Method.xls”) contain “Comment […]” columns (e.g., “Comment[primary particle measurements]”) designed to record whether or not the reported data are noted to refer to the primary particles (as opposed to agglomerates and/or aggregates) by the authors of the reference from which the data were extracted.
hydrophobicity	“m_MaterialSourceName.xls”; “a_InvID_PC_logP_Method.xls”	—