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.
Highlights
Nanotechnology, which may be considered the design and application of engineered nanomaterials with desired properties [1,2], is of increasing importance [3,4]
These resources are as follows: a collection of Excel templates for creating ISA-TAB-Nano files containing specific, relevantdata manually harvested from the scientific literature; a corresponding set of business rules for populating these templates which build upon the generic ISA-TAB-Nano specification; a Python program for converting the resulting ISA-TABNano files to tab-delimited text files to facilitate computational analysis and database submission
Within the NanoPUZZLES project [33], a number of project specific business rules were created for the purpose of specifying how the ISA-TAB-Nano templates described in section 3 should be populated with data from literature sources
Summary
Nanotechnology, which may be considered the design and application of engineered nanomaterials with desired properties [1,2], is of increasing importance [3,4]. In order to make most effective use of these data, experimental datasets should be made available via a standardised, electronic format that facilitates meaningful exchange of information between different researchers, submission to (web-based) searchable databases, integration with other electronic data resources and analysis via appropriate (modelling) software [9,16,17,18]. This article presents a set of resources which were designed for manually harvesting data from the published literature to create ISA-TAB-Nano datasets in order to support analysis and modelling of nanotoxicology data, including the integration of these data within online, searchable databases These resources are as follows: a collection of Excel templates for creating ISA-TAB-Nano files containing specific, relevant (meta)data manually harvested from the scientific literature; a corresponding set of business rules for populating these templates which build upon the generic ISA-TAB-Nano specification; a Python program for converting the resulting ISA-TABNano files to tab-delimited text files to facilitate computational analysis and database submission. The resources described in this article, along with the “Toy Dataset”, are publicly available under open licenses (see Supporting Information Files 1–4)
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