An ISA-TAB-Nano based data collection framework to support data-driven modelling of nanotoxicology

Abstract

Analysis of trends in nanotoxicology data and the development of data driven models for nanotoxicity is facilitated by the reporting of data using a standardised electronic format. ISA-TAB-Nano has been proposed as such a format. However, in order to build useful datasets according to this format, a variety of issues has to be addressed.These issues include questions regarding exactly which (meta)data to report and how to report them. The current article discusses some of the challenges associated with the use of ISA-TAB-Nano and presents a set of resources designed to facilitate the manual creation of ISA-TAB-Nano datasets from the nanotoxicology literature. These resources were developed within the context of the NanoPUZZLES EU project and include data collection templates, corresponding business rules that extend the generic ISA-TAB-Nano specification as well as Python code to facilitate parsing and integration of these datasets within other nanoinformatics resources. The use of these resources is illustrated by a "Toy Dataset" presented in the Supporting Information. The strengths and weaknesses of the resources are discussed along with possible future developments.

Perspectives from the NanoSafety Modelling Cluster on the validation criteria for (Q)SAR models used in nanotechnology

“…Indeed, this approach has been applied in recent nano-QSAR studies (Cassano et al, 2016;. Of course, in order to assess whether data are likely to be sufficiently inconsistent for their merging to be inadvisable or so that the inconsistency can be captured via treating the experimental variables as descriptors, it is crucial that the key experimental variables are consistently reported across data sources, which can be supported by use of ontologies (Hastings et al, 2015;Marchese Robinson et al, 2015). Indeed, the wider need for minimum reporting standards is currently a key topic in the nanoscience community (Aberg, 2015;Marchese Robinson et al, 2016;Marquardt et al, 2013;Stefaniak et al, 2013).…”

“…Given this structural complexity, it follows that representation formats for nanomaterials are definitely more complicated than those of single-molecule chemicals, and consequently this subject deserves separate and careful assessment. One such proposed format is the ISA-TAB-Nano Material file and its associated data files (Marchese Robinson et al, 2015;Thomas et al, 2013). The format used to represent the nanomaterial, even before starting any descriptor calculation, may have huge impact on the final model and therefore should be carefully specified.…”

“…Future work should consider whether the existing model reporting formats can be supplemented with links to suitable representations of nanomaterial structures, e.g. based on the Material file of ISA-TAB-Nano and linked data files (Burello, 2017;Marchese Robinson et al, 2015;Thomas et al, 2013), to better support the reproducibility and re-use of nano-QSAR models.…”

How should the completeness and quality of curated nanomaterial data be evaluated?

“…In the nanoscience area, the validation tools 111 developed within the MODERN E.U. FP7 project, 112 used to validate ISA-TAB-Nano datasets based on their compliance with the ISA-TAB-Nano specification, [113][114][115] were, to the best of the authors' knowledge, the only such tools available at the time of writing which were specifically developed for validating curated nanomaterial datasets.…”

“…[142][143][144] All of these software programs are potentially relevant to automatically validating nanomaterial characterisation and/or biological data. The ISA-TAB format [151][152][153] was recently extended via the development of ISA-TAB-Nano [113][114][115] to better capture nanomaterial (meta)data, so the ISA-Tools 139,140 software might be extended to validate ISA-TAB-Nano datasets. (As is discussed in section 3.2, some software for validating ISA-TAB-Nano files already exists.)…”