title: 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.
authors.affiliation: School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool, L3 3AF, United Kingdom.
authors.forename: Richard L
authors.initials: RL
authors.lastname: Marchese Robinson
authors.affiliation: School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool, L3 3AF, United Kingdom.
authors.forename: Mark T D
authors.initials: MT
authors.lastname: Cronin
authors.affiliation: School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool, L3 3AF, United Kingdom.
authors.forename: Andrea-Nicole
authors.initials: AN
authors.lastname: Richarz
authors.affiliation: Departament d'Enginyeria Informatica i Matematiques, Universitat Rovira i Virgili, Av. Paisos Catalans 26, 43007 Tarragona, Catalunya, Spain.
authors.forename: Robert
authors.initials: R
authors.lastname: Rallo
keywords: ISA-TAB-Nano; databases; nanoinformatics; nanotoxicology; quantitative structure–activity relationship (QSAR)